[gmx-users] ref_temp and gen_temp during simulated annealing
Hello users, I have some doubt regarding the reference temperature(ref_temp)option during simulated annealing, i mean in the .mdp for simulated annealing what should be the correct ref_temp i.e. 0 K(starting temerature) or the target temperature(328K) and accordingly what should be the value for gen_temp(0K or 328K). The part of my mdp file for the simulated annealing is as follows: ;Annealing annealing=single annealing_temp=0 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 328 annealing_npoints=18 annealing_time=0 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 ;Temperature coupling is on in two groups Tcoupl= V-rescale tau_t= 0.1 tc-grps= System ref_t= 328 pbc= xyz ; 3-D PBC ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT compressibility= 4.5e-5 ; Generate velocites is on at 328 K. gen_vel= yes ; assign velocities from Maxwell distribution gen_temp= 328.0 ; temperature for Maxwell distribution gen_seed= 173529;generate a random seed -- * - Thanks and regards Bipin Singh * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Conatant pH simulation in GROMACS
Hi all, I want to know that, whether we I can do constant pH simulation in gromacs. Please provide some details regarding this. -- * - Thanks and regards Bipin Singh * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_covar to calculate correlation of motion
Dear GMX users, I want to calculate the correlated motion between atoms during the md simulation for that purpose I am using g_covar(the one which is available under http://www.gromacs.org/Downloads/User_contributions/Other_software) but it is not compatible with the GROMACS-4.5.3, so please suggest me the alternative way or does anyone have the modified g_covar for GROMKACS-4.5.3. -- * - Thanks and regards Bipin Singh * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_covar to calculate correlation of motion
Hi, Thanks for your suggestion. While running the g_covar it is showing the error that aminoacids.dat is not found, so i have copied the residuetypes.dat(which i seems the new modified name for aminoacids.dat in current GROMACS version), then it prompts to choose the group for least square fit, which is not usual groups(i.e protein or C alpha groups etc.).please suggest where i have made mistake. Choose a group for the least squares fit Opening library file aminoacids.dat WARNING 2 [file aminoacids.dat, line 1]: File aminoacids.dat is empty Group 0 ( System) has 30585 elements Group 1 ( GLU) has47 elements Group 2 ( HIS) has86 elements Group 3 ( ASN) has 224 elements Group 4 ( PRO) has56 elements Group 5 ( VAL) has 272 elements Group 6 ( MET) has68 elements Group 7 ( GLY) has 168 elements Group 8 ( ILE) has 190 elements Group 9 ( ALA) has 110 elements Group10 ( SER) has 143 elements Group11 ( PHE) has80 elements Group12 ( LYS) has 242 elements Group13 ( TYR) has 189 elements Group14 ( LEU) has 304 elements Group15 ( GLN) has 102 elements Group16 ( TRP) has48 elements Group17 ( ARG) has 120 elements Group18 ( ASP) has 108 elements Group19 ( THR) has 141 elements Group20 ( SOL) has 27882 elements Group21 ( CL) has 5 elements On Mon, Feb 21, 2011 at 12:44, Tsjerk Wassenaar wrote: > Hi Bipin, > > Try using a .gro or .pdb file as reference structure (-s). Only .tpr files > are version specific. > > Cheers, > > Tsjerk > > On Feb 21, 2011 8:05 AM, "bipin singh" wrote: > > Dear GMX users, > I want to calculate the correlated motion between atoms during the md > simulation > > for that purpose I am using g_covar(the one which is available under > http://www.gromacs.org/Downloads/User_contributions/Other_software) > > > but it is not compatible with the GROMACS-4.5.3, so please suggest me the > alternative way or does anyone have the modified g_covar for > GROMKACS-4.5.3. > > -- > * > - > Thanks and regards > Bipin Singh > * > * > * > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- * - Thanks and regards Bipin Singh * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_covar to calculate correlation of motion
Thanks a lot Sir. On Mon, Feb 21, 2011 at 15:26, Tsjerk Wassenaar wrote: > Hi Bipin, > > The file residuetypes.dat is quite different from aminoacids.dat. You > can paste the following into that file (first line is number of > entries, followed by so many residue names): > > 49 > ABU > ACE > AIB > ALA > ARG > ARGN > ASN > ASN1 > ASP > ASP1 > ASPH > CYS > CYS1 > CYS2 > CYSH > DALA > GLN > GLU > GLUH > GLY > HIS > HIS1 > HISA > HISB > HISH > HYP > ILE > LEU > LYS > LYSH > MELEU > MET > MEVAL > NAC > NH2 > PHE > PHEH > PHEU > PHL > PRO > SER > THR > TRP > TRPH > TRPU > TYR > TYRH > TYRU > VAL > > > Groetjes, > > Tsjerk > > On Mon, Feb 21, 2011 at 8:47 AM, bipin singh wrote: > > Hi, > > Thanks for your suggestion. > > While running the g_covar it is showing the error that aminoacids.dat is > not > > found, so i have copied the residuetypes.dat(which i seems the new > modified > > name for aminoacids.dat in current GROMACS version), then it prompts to > > choose the group for least square fit, which is not usual groups(i.e > protein > > or C alpha groups etc.).please suggest where i have made mistake. > > > > Choose a group for the least squares fit > > Opening library file aminoacids.dat > > WARNING 2 [file aminoacids.dat, line 1]: > > File aminoacids.dat is empty > > Group 0 ( System) has 30585 elements > > Group 1 ( GLU) has47 elements > > Group 2 ( HIS) has86 elements > > Group 3 ( ASN) has 224 elements > > Group 4 ( PRO) has56 elements > > Group 5 ( VAL) has 272 elements > > Group 6 ( MET) has68 elements > > Group 7 ( GLY) has 168 elements > > Group 8 ( ILE) has 190 elements > > Group 9 ( ALA) has 110 elements > > Group10 ( SER) has 143 elements > > Group11 ( PHE) has80 elements > > Group12 ( LYS) has 242 elements > > Group13 ( TYR) has 189 elements > > Group14 ( LEU) has 304 elements > > Group15 ( GLN) has 102 elements > > Group16 ( TRP) has48 elements > > Group17 ( ARG) has 120 elements > > Group18 ( ASP) has 108 elements > > Group19 ( THR) has 141 elements > > Group20 ( SOL) has 27882 elements > > Group21 ( CL) has 5 elements > > > > > > On Mon, Feb 21, 2011 at 12:44, Tsjerk Wassenaar > wrote: > >> > >> Hi Bipin, > >> > >> Try using a .gro or .pdb file as reference structure (-s). Only .tpr > files > >> are version specific. > >> > >> Cheers, > >> > >> Tsjerk > >> > >> On Feb 21, 2011 8:05 AM, "bipin singh" wrote: > >> > >> Dear GMX users, > >> > >> I want to calculate the correlated motion between atoms during the md > >> simulation > >> > >> for that purpose I am using g_covar(the one which is available under > >> http://www.gromacs.org/Downloads/User_contributions/Other_software) > >> > >> > >> > >> but it is not compatible with the GROMACS-4.5.3, so please suggest me > the > >> alternative way or does anyone have the modified g_covar for > >> GROMKACS-4.5.3. > >> > >> -- > >> - > >> Thanks and regards > >> Bipin Singh > >> > >> > >> -- > >> gmx-users mailing listgmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> -- > >> gmx-users mailing listgmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] H-bond autocorrelation doubts
Hello, I am usng g_hbond to calculate H bond auto correlation during the simulation for two residues in my system, I have two doubts regarding this: 1)How to use -acflen to calculate autocorrelation for all the frames instead of half of the frames 2) What is the use of -temp option in calculating the autocorrelation because it is giving same result whether you use 298K or 500K I have read the manual but I am not clear about these functions. -- * - Thanks and regards Bipin Singh * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] H-bond autocorrelation doubts
Thanks for your suggestions. Can you please give some explanation for my second doubt... 2011/2/28 André Farias de Moura > the manual does not enclose all the necessary knowledge for any kind of MD > simulation or analyses, so you have to read some papers and textbooks as > well.as I've already pointed out, g_hbond reads the whole set of frames, > but the > results are meaningful (in the sense of having a homogeneous variance) only > up to half of the size of the sample. if you need the correlation > function for a > longer time lag, increase the length of your simulation. that way, your ACF > should remain meaningful. > > best > > Andre > > On Mon, Feb 28, 2011 at 10:36 AM, bipin singh > wrote: > > > > Hello, > > > > I am usng g_hbond to calculate H bond auto correlation during the > simulation > > for two residues in my system, I have two doubts regarding this: > > > > 1)How to use -acflen to calculate autocorrelation for all the frames > instead > > of half of the frames > > 2) What is the use of -temp option in calculating the autocorrelation > > because it is giving same result whether you use 298K or 500K > > > > I have read the manual but I am not clear about these functions. > > -- > > - > > Thanks and regards > > Bipin Singh > > > > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- * - Thanks and regards Bipin Singh * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] H-bond autocorrelation doubts
NO, its giving same result no matter what temperature you provide using -temp option. On Mon, Feb 28, 2011 at 23:55, Erik Marklund wrote: > It computes the same acf, but the thermodynamic/kinetic calculations give > different results for different -temp, don't they? > > Erik > > bipin singh skrev 2011-02-28 18.01: > > Thanks for your suggestions. > Can you please give some explanation for my second doubt... > > 2011/2/28 André Farias de Moura > >> the manual does not enclose all the necessary knowledge for any kind of MD >> simulation or analyses, so you have to read some papers and textbooks as >> well.as I've already pointed out, g_hbond reads the whole set of frames, >> but the >> > results are meaningful (in the sense of having a homogeneous variance) >> only >> up to half of the size of the sample. if you need the correlation >> function for a >> longer time lag, increase the length of your simulation. that way, your >> ACF >> should remain meaningful. >> >> best >> >> Andre >> >> On Mon, Feb 28, 2011 at 10:36 AM, bipin singh >> wrote: >> > >> > Hello, >> > >> > I am usng g_hbond to calculate H bond auto correlation during the >> simulation >> > for two residues in my system, I have two doubts regarding this: >> > >> > 1)How to use -acflen to calculate autocorrelation for all the frames >> instead >> > of half of the frames >> > 2) What is the use of -temp option in calculating the autocorrelation >> > because it is giving same result whether you use 298K or 500K >> > >> > I have read the manual but I am not clear about these functions. >> > -- >> > - >> > Thanks and regards >> > Bipin Singh >> > >> > >> > -- >> > gmx-users mailing listgmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> > Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to gmx-users-requ...@gromacs.org. >> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > * > - > Thanks and regards > Bipin Singh > * > * > * > > > > -- > --- > Erik Marklund, PhD student > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596,75124 Uppsala, Sweden > phone:+46 18 471 4537fax: +46 18 511 755er...@xray.bmc.uu.se > http://folding.bmc.uu.se/ > > -- * - Thanks and regards Bipin Singh * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Error during PUMED installation for GROMACS-4.5.3
/restraint_alpharmsd.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_angle.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_antibetarmsd.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_coord.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_dihcor.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_dipole.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_dist.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_elstpot.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_energy.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_hbonds.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_helix.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_mindist.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_parabetarmsd.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_position.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_puckering.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_rgyr.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_rmsdtor.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_spath.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_torsion.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_waterbridge.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_zpath.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/testderivatives.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/*.Po': No such file or directory - DONE! -- * - Thanks and regards Bipin Singh * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding DCCM analysis with g_covar available in user contributed section
Hello, I am using g_covar vailable in user contributed section (by Ran Friedman) the description available for the package is as follows: "This package contains a modified version of g_covar, which can print a matrix of atomic correlation coefficients (with -xpmc) and write all pairs with a correlation > 0.5 to a log file (with -clog). Otherwise it is the same as the original program. The xpm correlation matrix shows only cross-correlations larger than 0.5 (absolute values) on the upper triangle and all values on the lower triangle. Thus, the upper triangle displays only the most correlated motions." As stated that the upper triangle only shows the cross-correlation greater than 0.5, but I am also getting some negative correlation values(blue regions) in above triangle. I don't know what is the region behind this. Plz help me to understand this behaviour. I have attached my xpm matrix file generated using g_covar. -- * - Thanks and regards Bipin Singh * * * <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding editconf
I have some questions regarding editconf: 1)If we did'nt mentioned -box parameters,the *default vectors are 0 0 0*, why it is zero and what does it mean? 2)How to determine distance between the solute and the box, is it appropriate to take it 0.9 nm for a globular protein of 179 amino acids. After running editconf using the command *editconf -bt cubic -f 1.pdb -o 2.pdb -c -d 0.9* I got the following output: Read 3256 atoms Volume: 515.892 nm^3, corresponds to roughly 232100 electrons No velocities found system size : 4.217 4.721 4.631 (nm) diameter : 5.270 (nm) center : 1.974 2.562 0.035 (nm) box vectors : 7.602 7.602 10.309 (nm) box angles : 90.00 90.00 120.00 (degrees) box volume : 515.89 (nm^3) shift: 1.562 0.973 3.500 (nm) new center : 3.535 3.535 3.535 (nm) new box vectors : 7.070 7.070 7.070 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 353.45 (nm^3) I have some question regarding this output: 1)Why new box volume decreased?And what does it mean? 2)Why the new length of box vectors decreased?And what does it mean? 3)How gromacs assign vectors length?If not provided in the editconf command. 4)How gromacs place solvent inside the box(genbox) , I mean using which method and how gromacs determine the the number of solvent to be placed inside the box. --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding the construction of Dynamics cross correlation map from covar.dat(from g_covar)
Hello users, Although there was already much discussion had been done on the procedure to construct DCCM map from covar.dat(i.e. output from g_covar) but still I am not clear with the step wise procedure to calculate the correlation matrix from covarience matrix(covar.dat). 1) It is stated in the previous posts that to calculate correlation matrix we have to divide each i,j-th element of the covariance matrix (covar.dat) by the sqrt of the ii-th and jj-th diagonal element, but how to get diagonal of a 865107X3 matrix??? 2) As given in the manual the order of elements in covar.dat is is: x1x1,x1y1, x1z1, x1x2, ... But I am not clear which are i,j-th ,ii-th and jj-th elements in covar.dat. My covarience matrix have 865107 rows and 3 columns and the total atoms are 537(sqrt( 865107 X 3) / 3=537 atoms) Can anyone suggest how to transform the covar.dat into correlation matrix. I am expecting the stepwise procedure to construct the correlation matrix and not the theory behind it as it already stated in the previous posts. -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding the construction of Dynamics cross correlation map from covar.dat(from g_covar)
Hello users, Although there was already much discussion had been done on the procedure to construct DCCM map from covar.dat(i.e. output from g_covar) but still I am not clear with the step wise procedure to calculate the correlation matrix from covarience matrix(covar.dat). 1) It is stated in the previous posts that to calculate correlation matrix we have to divide each i,j-th element of the covariance matrix (covar.dat) by the sqrt of the ii-th and jj-th diagonal element, but how to get diagonal of a 865107X3 matrix??? 2) As given in the manual the order of elements in covar.dat is is: x1x1,x1y1, x1z1, x1x2, ... But I am not clear which are i,j-th ,ii-th and jj-th elements in covar.dat. My covarience matrix have 865107 rows and 3 columns and the total atoms are 537(sqrt( 865107 X 3) / 3=537 atoms) Can anyone suggest how to transform the covar.dat into correlation matrix. I am expecting the stepwise procedure to construct the correlation matrix and not the theory behind it as it already stated in the previous posts. regards Bipin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Which structure to be used during covariance analysis
Hello, I just want to know which structure to be used during covariance analysis with g_covar with -s flag(As stated in manual:All structures are fitted to the structure in the structure file), So which of the following structure would be appropriate to choose for covariance analysis, If we want to calculate covariance during the simulation(Production run) (i) Structure after energy minimization (ii)Structure after equilibration (iii)Original crystal structure -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Which structure to be used during covariance analysis
> Hello, > I just want to know which structure to be used during covariance analysis > with g_covar with > -s flag(As stated in manual:All structures are fitted to the structure in > the structure file), > So which of the following structure would be appropriate to choose for > covariance analysis, > If we want to calculate covariance during the simulation(Production run) > > (i) Structure after energy minimization > (ii)Structure after equilibration > (iii)Original crystal structure > -- > ------- > *Regards,* > Bipin Singh > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Which structure to be used during covariance analysis
Thanks Sir for you help regarding the doubt On Tue, Mar 29, 2011 at 22:49, Tsjerk Wassenaar wrote: > Hi Bipin, > > That won't really matter. The reference is just for fitting. > > Cheers, > > Tsjerk > > On Mar 29, 2011 3:51 PM, "bipin singh" wrote: > > > > Hello, > I just want to know which structure to be used during > covariance analysis with g_cov... > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding g_enemat
Hello, I am using g_enemat to calculate the energy matrix from the energy file(edr file) and I am supplying Protein as a group in -groups option. The command I am supplied is as follows: g_enemat -f file.edr -groups groups.dat -emat emat.xpm -etot energy.xvg -temp 328 -nocoul -nolj -nomean but I am getting the following error Read 1 groups group 0WARNING! could not find group (null):Protein-Protein (0,0)in energy file As written in the manual: "Energy groups with names like ’Coul-SR:Protein-SOL’ and ’LJ:Protein-SOL’ are expected in the energy file" But I am not clear how to get these terms in energy file. The energy file I am supplying is from a 100 ns md simulation. -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding g_enemat
Thanks for your reply The following terms are present in my energy files 1 Angle2 Proper-Dih. 3 Improper-Dih.4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 Disper.-corr.8 Coulomb-(SR) 9 Coul.-recip.10 Potential 11 Kinetic-En. 12 Total-Energy 13 Temperature 14 Pres.-DC15 Pressure16 Constr.-rmsd 17 Box-X 18 Box-Y 19 Box-Z 20 Volume 21 Density 22 pV23 Enthalpy24 Vir-XX 25 Vir-XY 26 Vir-XZ27 Vir-YX 28 Vir-YY 29 Vir-YZ 30 Vir-ZX 31 Vir-ZY 32 Vir-ZZ 33 Pres-XX 34 Pres-XY 35 Pres-XZ 36 Pres-YX 37 Pres-YY 38 Pres-YZ 39 Pres-ZX 40 Pres-ZY 41 Pres-ZZ 42 #Surf*SurfTen 43 Box-Vel-XX 44 Box-Vel-YY 45 Box-Vel-ZZ 46 Mu-X47 Mu-Y48 Mu-Z 49 T-Protein 50 T-non-Protein 51 Lamb-Protein 52 Lamb-non-Protein So, please suggest why I am getting error, If the LJ-(SR) and Coulomb-(SR) terms are already present in the energy file. On Thu, Apr 14, 2011 at 00:36, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Hello, >> >> I am using g_enemat to calculate the energy matrix from the energy >> file(edr file) and I am supplying Protein as a group in -groups >> option. >> The command I am supplied is as follows: >> >> g_enemat -f file.edr -groups groups.dat -emat emat.xpm -etot >> energy.xvg -temp 328 -nocoul -nolj -nomean >> >> but I am getting the following error >> Read 1 groups >> group 0WARNING! could not find group (null):Protein-Protein (0,0)in energy >> file >> >> As written in the manual: >> "Energy groups with names like ’Coul-SR:Protein-SOL’ and >> ’LJ:Protein-SOL’ are expected in the energy >> file" >> But I am not clear how to get these terms in energy file. >> > > Whatever name you supply has to be an actual term in the .edr file. Run > g_energy first to get a list of all valid energy terms if you are unfamiliar > with the contents of the .edr file. > > -Justin > >> The energy file I am supplying is from a 100 ns md simulation. >> > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to get angle distribution between two tyrosine stacking residues
Hello users, Can anyone tell how to calculate the normal-normal angle between two stacking tyrosine residues as a function of time. -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] compilation of g_hbond after bugfix
Hello,
I want to compile the source code gmx_hbond.c after the below
mentioned bugfix, I have already installed gromacs 4.5.3, how can I
compile only gmx_hbond.c in already installed
gromacs 4.5.3.
>Hi,
>There have been reports about inconsistencies between older (<= 4.0.7?) and
>newer versions of g_hbond, where the older seem to have been more reliable. I
>found and killed the bug >that caused the newer versions to miscount the
>hbonds. Checkout release-4-5-patches to get the bugfix, or patch it yourself
>by commenting out line 1497, which reads "return hbNo;":
> if (bBox){
>if (d>a && bMerge && (bContact || isInterchangable(hb, d, a, grpd, grpa))) {
>/* acceptor is also a donor a\
>nd vice versa? */
>/* return hbNo; */
>daSwap = TRUE; /* If so, then their history should be filed with donor and
>acceptor swapped. */
> }
>Simple as that
--
---
Thanks & Regards,
Bipin Singh
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Error in energy group exclusion
Hello users, I am getting the following warning during the grompp - WARNING 1 [file md.mdp]: Can not exclude the lattice Coulomb energy between energy groups --- I am providing the following energy groups and energy exclusion group in my mdp file energygrps=Protein SOL energygrp_excl=Protein Protein SOL SOL Please suggest me, why I am getting the above error and how to get rid of this error. -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error in energy group exclusion
Thanks for your reply, I have already done with the final simulation, and now if I have to change the method for electrostatic calculation(instead of PME) for energy group exclusion, then will it make sense i.e. how consistent it would be with my simulation results(with PME). Please suggest.. On Mon, May 23, 2011 at 21:28, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Hello users, >> I am getting the following warning during the grompp >> >> - >> WARNING 1 [file md.mdp]: >> Can not exclude the lattice Coulomb energy between energy groups >> >> --- >> >> I am providing the following energy groups and energy exclusion group >> in my mdp file >> energygrps=Protein SOL >> energygrp_excl=Protein Protein SOL SOL >> >> Please suggest me, why I am getting the above error and how to get rid >> of this error. >> > > Presumably you're using PME for long-range electrostatics. The message > you're getting is grompp trying to help you realize that with PME it is not > possible to completely exclude all energetic terms, since the long-range > mesh is always calculated. Only short-range nonbonded interactions (LJ and > Coulombic terms) are excluded in the mechanism above. > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error in energy group exclusion
Thanks for your reply, Yes, you are correct, I want calculate the non-bonded interaction energies terms for Protein-Protein and Protein-Solvent system using rerun of the trajectory from a already finished simulation (using PME method).Please suggest whether there is any way to get these terms. On Mon, May 23, 2011 at 23:06, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Thanks for your reply, >> I have already done with the final simulation, and now if I have to >> change the method for electrostatic calculation(instead of PME) >> for energy group exclusion, then will it make sense i.e. how >> consistent it would be with my simulation results(with PME). >> Please suggest.. >> > > I'm not 100% clear on what you're doing, but I assume you're trying to do > some rerun of a trajectory to calculate various energy components? If > that's the case, there is a wealth of discussion on this topic in the list > archive. It is generally an exercise in futility or ambiguity. If a > trajectory was generated using long-range methods like PME, what sense is it > to re-calculate some component of the the energies of configurations that > were created using a different method? The long-range terms may have a > significant impact on the dynamical behavior, which you're now ignoring. > > If this is not your intent, then please explain further. > > -Justin > >> On Mon, May 23, 2011 at 21:28, Justin A. Lemkul wrote: >>> >>> bipin singh wrote: >>>> >>>> Hello users, >>>> I am getting the following warning during the grompp >>>> >>>> >>>> - >>>> WARNING 1 [file md.mdp]: >>>> Can not exclude the lattice Coulomb energy between energy groups >>>> >>>> >>>> --- >>>> >>>> I am providing the following energy groups and energy exclusion group >>>> in my mdp file >>>> energygrps=Protein SOL >>>> energygrp_excl=Protein Protein SOL SOL >>>> >>>> Please suggest me, why I am getting the above error and how to get rid >>>> of this error. >>>> >>> Presumably you're using PME for long-range electrostatics. The message >>> you're getting is grompp trying to help you realize that with PME it is >>> not >>> possible to completely exclude all energetic terms, since the long-range >>> mesh is always calculated. Only short-range nonbonded interactions (LJ >>> and >>> Coulombic terms) are excluded in the mechanism above. >>> >>> -Justin >>> >>> -- >>> >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface >>> or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> > > -- > ======== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding calculation of Salt bridge between specific group of atoms
Dear all, I want to calculate the salt bridge interaction between a particular set of residues, because I can not use index file with g_saltbr, so the next options available are g_dist and g_mindist. As stated in manual g_dist gives the distance between the center of mass of two groups of atom, while g_mindist gives us the minimum distance between any pair of atom. My doubt is that which distance(either given by g_dist or g_mindist) corresponds to the salt bridge interaction distance between two atoms. -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding calculation of Salt bridge between specific group of atoms
Thanks Sir, I understood.. On Sat, Jun 11, 2011 at 17:30, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Dear all, >> >> I want to calculate the salt bridge interaction between a particular >> set of residues, >> because I can not use index file with g_saltbr, so the next options >> available are >> g_dist and g_mindist. As stated in manual g_dist gives the distance >> between the >> center of mass of two groups of atom, while g_mindist gives us the minimum >> distance between any pair of atom. >> My doubt is that which distance(either given by g_dist or g_mindist) >> corresponds to the salt bridge interaction distance >> between two atoms. > > Not necessarily either. g_dist measures COM distances between the given > index groups, and g_mindist measures the minimum distance of any atom pair, > which, for a multi-atom index group, may change over time. > > The solution is to create specific index groups. If you want the distance > between two specific atoms, create two index groups of one atom each and use > g_dist (or g_mindist, because in this case the output would be identical). > If you want the distance between, e.g. the amino group of lysine and the > carboxylate of glutamate, then the amine group with have four atoms (NZ, > HZ1, HZ2, HZ3) and the carboxylate group will have 3 (CD, OE1, OE2). Then > use g_dist. > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding H-bond autocorrelation
Hello, I am calculating the H-bond autocorrelation using g_hbond for my system, but after plotting I have observed that the value for c(t) is reaching to negative, as far as I know it can not be negative as the probability can not be negative...please suggest where is the problem.. -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding H-bond autocorrelation
Hello, I am calculating the H-bond autocorrelation using g_hbond for my system, but after plotting I have observed that the value for c(t) is reaching to negative, as far as I know it can not be negative as the probability can not be negative...please suggest where is the problem.. -- --- Thanks and Regards, Bipin Singh -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding H-bond autocorrelation
I am using the Gromacs 4.5.3is that feature is present in this version.. On Mon, Jun 13, 2011 at 21:39, Erik Marklund wrote: > Hi, > > The problem is that g_hbond subtracts a "background level" to compensate for > the finite size of the system. I thought that feature had been taken away, > however. Are you using old code? > > Erik > > 12 jun 2011 kl. 19.33 skrev bipin singh: > >> Hello, >> >> I am calculating the H-bond autocorrelation using g_hbond for my >> system, but after plotting >> I have observed that the value for c(t) is reaching to negative, as >> far as I know it can not be >> negative as the probability can not be negative...please suggest >> where is the problem.. >> >> -- >> --- >> Thanks and Regards, >> Bipin Singh >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > --- > Erik Marklund, PhD student > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > er...@xray.bmc.uu.se > http://www2.icm.uu.se/molbio/elflab/index.html > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding H-bond autocorrelation
Thanks Sir,for your reply... I have a silly question regarding the g_hbond's autocorrelation output: The output contains the following four columns (i) Ac fin sys(t) (ii) Ac(t) (iii) Cc contact,hb(t) (iv) -dAc fs/dt As I understood the first column is the acf with background subtraction,and the second column is acf without background subtraction.Can you please refer some text from where I could get the details about the above mentioned output options and their importance in in H-bond dynamics. On Tue, Jun 14, 2011 at 16:53, Erik Marklund wrote: > Could be. But, if memory serves me right, there's another dataset in the > output, which shows the acf without the "background subtraction". > > Erik > > 14 jun 2011 kl. 12.10 skrev bipin singh: > >> I am using the Gromacs 4.5.3is that feature is present in >> this version.. >> >> On Mon, Jun 13, 2011 at 21:39, Erik Marklund wrote: >>> Hi, >>> >>> The problem is that g_hbond subtracts a "background level" to compensate >>> for the finite size of the system. I thought that feature had been taken >>> away, however. Are you using old code? >>> >>> Erik >>> >>> 12 jun 2011 kl. 19.33 skrev bipin singh: >>> >>>> Hello, >>>> >>>> I am calculating the H-bond autocorrelation using g_hbond for my >>>> system, but after plotting >>>> I have observed that the value for c(t) is reaching to negative, as >>>> far as I know it can not be >>>> negative as the probability can not be negative...please suggest >>>> where is the problem.. >>>> >>>> -- >>>> --- >>>> Thanks and Regards, >>>> Bipin Singh >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>> Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> --- >>> Erik Marklund, PhD student >>> Dept. of Cell and Molecular Biology, Uppsala University. >>> Husargatan 3, Box 596, 75124 Uppsala, Sweden >>> phone: +46 18 471 4537 fax: +46 18 511 755 >>> er...@xray.bmc.uu.se >>> http://www2.icm.uu.se/molbio/elflab/index.html >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> >> -- >> --- >> Regards, >> Bipin Singh >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > --- > Erik Marklund, PhD student > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > er...@xray.bmc.uu.se > http://www2.icm.uu.se/molbio/elflab/index.html > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding H-bond autocorrelation
Thanks Sir,for your reply... I have a silly question regarding the g_hbond's autocorrelation output: The output contains the following four columns (i) Ac fin sys(t) (ii) Ac(t) (iii) Cc contact,hb(t) (iv) -dAc fs/dt As I understood the first column is the acf with background subtraction,and the second column is acf without background subtraction.Can you please refer some text from where I could get the details about the above mentioned output options and their importance in in H-bond dynamics. On Tue, Jun 14, 2011 at 16:53, Erik Marklund wrote: > Could be. But, if memory serves me right, there's another dataset in the > output, which shows the acf without the "background subtraction". > > Erik > > 14 jun 2011 kl. 12.10 skrev bipin singh: > >> I am using the Gromacs 4.5.3is that feature is present in >> this version.. >> >> On Mon, Jun 13, 2011 at 21:39, Erik Marklund wrote: >>> Hi, >>> >>> The problem is that g_hbond subtracts a "background level" to compensate >>> for the finite size of the system. I thought that feature had been taken >>> away, however. Are you using old code? >>> >>> Erik >>> >>> 12 jun 2011 kl. 19.33 skrev bipin singh: >>> >>>> Hello, >>>> >>>> I am calculating the H-bond autocorrelation using g_hbond for my >>>> system, but after plotting >>>> I have observed that the value for c(t) is reaching to negative, as >>>> far as I know it can not be >>>> negative as the probability can not be negative...please suggest >>>> where is the problem.. >>>> >>>> -- >>>> --- >>>> Thanks and Regards, >>>> Bipin Singh >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>> Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> --- >>> Erik Marklund, PhD student >>> Dept. of Cell and Molecular Biology, Uppsala University. >>> Husargatan 3, Box 596, 75124 Uppsala, Sweden >>> phone: +46 18 471 4537 fax: +46 18 511 755 >>> er...@xray.bmc.uu.se >>> http://www2.icm.uu.se/molbio/elflab/index.html >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> >> -- >> --- >> Regards, >> Bipin Singh >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > --- > Erik Marklund, PhD student > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > er...@xray.bmc.uu.se > http://www2.icm.uu.se/molbio/elflab/index.html > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- Regards, Bipin Singh -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] cross correlations
/gmx-users > >>> Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >>> Please don't post (un)subscribe requests to the list. Use the www > >>> interface > >>> or send it to gmx-users-requ...@gromacs.org. > >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >> > >> > >> > >> -- > >> Tsjerk A. Wassenaar, Ph.D. > >> > >> post-doctoral researcher > >> Molecular Dynamics Group > >> * Groningen Institute for Biomolecular Research and Biotechnology > >> * Zernike Institute for Advanced Materials > >> University of Groningen > >> The Netherlands > > > > -- > > Best Regards, > > Alexey 'Alexxy' Shvetsov > > Petersburg Nuclear Physics Institute, Russia > > Department of Molecular and Radiation Biophysics > > Gentoo Team Ru > > Gentoo Linux Dev > > mailto:alexx...@gmail.com > > mailto:ale...@gentoo.org > > mailto:ale...@omrb.pnpi.spb.ru > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the www > interface > > or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding g_dist -dist option
Hello, I just want to ask that in g_dist module, -dist option expect distance as a real argument, so the distance should be in nm or A for that... -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding g_dist -dist option
Thanks... On Fri, Jun 24, 2011 at 20:17, shivangi nangia wrote: > > > On Fri, Jun 24, 2011 at 10:45 AM, bipin singh wrote: > >> Hello, >> I just want to ask that in g_dist module, -dist option expect distance as >> a real argument, so the distance should be in nm or A for that... >> > > -nanometer (nm) > >> >> -- >> --- >> *Regards,* >> Bipin Singh >> >> >> -- >> >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] cross correlations
Thanks a lot Sir for your help. On Fri, Jun 24, 2011 at 22:54, Tsjerk Wassenaar wrote: > Hi Bipin, > > Read them in as a vector of numbers and divide them into sqrt(len(vector)) > rows to get yourself a nice square correlation matrix. > > Cheers, > > Tsjerk > > On Jun 24, 2011 3:28 PM, "bipin singh" wrote: > > Hello, > I have some doubts regarding the output file correl.dat as it contains 3 > columns, but I am not able to get what are > these column contains,I mean how to change it to the format in which I can > directly plot the data to get DCCM map... > For e.g in this form > Res1 Res2 Correlation coefficient > x yz > > On Sun, Jun 19, 2011 at 16:16, Tsjerk Wassenaar wrote: > > > Of course you did.. > --- > *Regards,* > Bipin Singh > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] cross correlations
Hello, I have calculated the covariance matrix for C-alpha atoms(179 aa) only,but after plotting the correlation, I have observed that it is of 537X537,instead of179X179.Please suggest me how to get correlation between the C-alpha atoms only. On Fri, Jun 24, 2011 at 22:54, Tsjerk Wassenaar wrote: > Hi Bipin, > > Read them in as a vector of numbers and divide them into sqrt(len(vector)) > rows to get yourself a nice square correlation matrix. > > Cheers, > > Tsjerk > > On Jun 24, 2011 3:28 PM, "bipin singh" wrote: > > Hello, > I have some doubts regarding the output file correl.dat as it contains 3 > columns, but I am not able to get what are > these column contains,I mean how to change it to the format in which I can > directly plot the data to get DCCM map... > For e.g in this form > Res1 Res2 Correlation coefficient > x yz > > On Sun, Jun 19, 2011 at 16:16, Tsjerk Wassenaar wrote: > > > Of course you did.. > --- > *Regards,* > Bipin Singh > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding DispCorr
Hello, Please let me know, Whether it is correct to use DispCorr=EnerPres during energy minimization. -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding DispCorr
Hello, Thanks for reply. As given in the manual, If we give DispCorr=EnerPres it will apply long range dispersion corrections for Energy and Pressure. But I don't know whether it is logical to apply this during energy minimization. On Sun, Feb 19, 2012 at 20:20, Mark Abraham wrote: > On 19/02/2012 11:21 PM, bipin singh wrote: >> >> Hello, >> >> Please let me know, Whether it is correct to use DispCorr=EnerPres >> during energy minimization. >> > > What does it do? > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding DispCorr
Thank you so much Sir for clearing my doubts. I understood your point. On Mon, Feb 20, 2012 at 12:51, Mark Abraham wrote: > On 20/02/2012 4:19 PM, bipin singh wrote: > >> Thanks for your help. But I am getting different results for potential >> energy when minimization done applying DispCorr=EnerPres and >> minimization done without DispCorr. Please provide your suggestions >> > > They will be different, but they are highly unlikely to be *significantly* > different. Slight changes in the nearly symmetric effect of long-range > interactions are not going to change the general nature of the local > minimum that you approach with EM - and decidedly not if all you are doing > is preparing to do dynamics. Doing those dynamics is a different matter. > > Mark > > > >> My mdp for minimization is as follows: >> >> define= -DFLEXIBLE >> constraints = none >> integrator= steep >> dt= 0.002; ps ! >> nsteps= 50 >> nstlist= 1 >> ns_type= grid >> rlist= 1.0 >> coulombtype= PME >> vdwtype= cut-off >> rcoulomb= 1.0 >> rvdw= 1.0 >> DispCorr=EnerPres ; (and No DispCorr for other case) >> fourierspacing= 0.12 >> fourier_nx= 0 >> fourier_ny= 0 >> fourier_nz= 0 >> pme_order= 4 >> ewald_rtol= 1e-5 >> optimize_fft= yes >> emtol=100.0 >> emstep=0.01 >> pbc=xyz >> >> >> On Mon, Feb 20, 2012 at 05:03, Mark >> Abraham> >> wrote: >> >>> On 20/02/2012 2:23 AM, bipin singh wrote: >>> >>>> Hello, >>>> Thanks for reply. >>>> As given in the manual, If we give DispCorr=EnerPres it will apply >>>> long range dispersion corrections for Energy and Pressure. >>>> But I don't know whether it is logical to apply this during energy >>>> minimization. >>>> >>> >>> Manual 4.8 sets out some conditions for its use. It is likely from the >>> nature of EM that it doesn't matter either way. >>> >>> Mark >>> >>> >>> On Sun, Feb 19, 2012 at 20:20, Mark >>> Abraham >>>> > >>>> wrote: >>>> >>>>> On 19/02/2012 11:21 PM, bipin singh wrote: >>>>> >>>>>> Hello, >>>>>> >>>>>> Please let me know, Whether it is correct to use DispCorr=EnerPres >>>>>> during energy minimization. >>>>>> >>>>>> What does it do? >>>>> >>>>> Mark >>>>> -- >>>>> gmx-users mailing listgmx-users@gromacs.org >>>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>> Please search the archive at >>>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >>>>> posting! >>>>> Please don't post (un)subscribe requests to the list. Use the www >>>>> interface >>>>> or send it to gmx-users-requ...@gromacs.org. >>>>> Can't post? Read >>>>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>>> >>>> >>>> >>>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> Please search the archive at >>> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface >>> or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read >>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> >> >> >> > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulated Annealing Protocol...
bar] >> reference pressure for coupling >> >> ; 7.3.17 Velocity Generation >> gen_vel = no ; velocity generation >> turned off >> gen_temp = 277 >> ; 7.3.18 Bonds >> constraints = all-bonds ; convert all bonds to constraints >> constraint_algorithm = LINCS ; LINear Constraint Solver >> continuation = yes ; apply constraints to the >> start configuration >> lincs_order = 4 ; highest order in the >> expansion of the contraint coupling matrix >> lincs_iter = 1 ; number of iterations to >> correct for rotational lengthening >> lincs_warnangle = 30 ; [degrees] maximum angle that >> a bond can rotate before LINCS will complain >> continuation =yes >> >> so my Queries are >> 1. As I not define = -DPOSRES in SA mdp is it sound well???, >> should I have to run Production run after my >> SA run(That means Is SA is substitute to Production run ??) >> ??? or I have to use define = -DPOSRES in my SA mdp , >> and then I have to do production run >> 2. Or as per Justin recommendation NVT at 277 ,followed by SA >> (Then I have to use define = -DPOSRES in My SA mdp file ,Is it >> right??) >> then NPT afterward Production run .. >> >> So what is your suggestion ??? > > > The answers to your question depend entirely upon what you want to do and > observe. If you're using SA simply as part of an equilibration protocol (as > I often do, which was what I based my suggestion upon earlier), then I stick > with my protocol, which is point #2. > > If you're trying to model the behavior of your system in response to a > change in termperature, then SA is your production run and you would not use > position restraints. > > It is still not clear to me how you wish to use SA or what you hope to > observe from it, so that's the best I can offer. > > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to add dihedral information from the GAFF topology
Hello all, I am using the GAFF topology provided for octan-1-ol at Gromacs liquid database (http://virtualchemistry.org/molecules/111-87-5/index.php). I have incorporated all the parameters for atoms, bonds and non-bonded interaction type in the forcefield (Amber99sb-ildn in Gromacs) from GAFF topology (111-87-5.top), but I am not sure how to add the dihedraltypes information in ffbonded.itp from the GAFF topology as to add this information I need the phase and kd for each dihedral. Is this information is available in the GAFF topology provided in the Gromacs database ? -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: How to add dihedral information from the GAFF topology
Thanks for your reply. But as far as I understood, in order to use these GAFF topology (for e.g. to perform simulation using these topologies) with Gromacs we have to incorporate the information from these topologies to the existing Amber forcefields in Gromacs or Is there anyway (Possibility of using Standalone GAFF parameters in Gromacs) to do it without performing this task. As you said these topologies are self supporting and we do not need to change ffbonded.itp, but during grompp I got the following error, may be because I have not added the dihedral information. ERROR [file oct.top]: No default Proper Dih. types Please provide your suggestions. On Mon, Mar 26, 2012 at 17:29, David van der Spoel wrote: > On 2012-03-26 13:55, bipin singh wrote: >> >> Hello all, >> >> I am using the GAFF topology provided for octan-1-ol at Gromacs liquid >> database (http://virtualchemistry.org/molecules/111-87-5/index.php). I >> have incorporated all the parameters >> for atoms, bonds and non-bonded interaction type in the forcefield >> (Amber99sb-ildn in Gromacs) from GAFF topology (111-87-5.top), but I >> am not sure how to add the dihedraltypes information in ffbonded.itp >> from the GAFF topology as to add this information I need the phase and >> kd for each dihedral. Is this information is available in the GAFF >> topology provided in the Gromacs database ? >> >> > > This topology is self supporting and you do not need anything else in > ffbonded.itp. > > You should be careful merging such parameters with an existing force field, > because strictly speaking these are different force fields. >> >> >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: How to add dihedral information from the GAFF topology
Thanks for your reply. Yes, you are right that these topologies are self supporting and there is no need to to call any other information. I followed your suggestions and able to generate a biphasic system of water/octane containing a protein molecule. But, when I tried grompp on this biphasic system (containing octane+water+protein), it results in error even if I include the topologies in forcefield.itp file. The error was Fatal error: Atomtype hc not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors On Mon, Mar 26, 2012 at 18:46, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Thanks for your reply. >> But as far as I understood, in order to use these GAFF topology (for >> e.g. to perform simulation using these topologies) with Gromacs we >> have to incorporate the information from these topologies to the >> existing Amber forcefields in Gromacs or Is there anyway (Possibility >> of using Standalone GAFF parameters in Gromacs) to do it without >> performing this task. >> > > As David said, the topologies stand on their own. You do not need to call > any further information from anywhere. The .top that you downloaded begins > with a [defaults] directive, declares atom types, and proceeds through the > rest of the topology with explicit parameters. > > >> As you said these topologies are self supporting and we do not need to >> change ffbonded.itp, but during grompp I got the following error, may >> be because I have not added the dihedral information. >> >> ERROR [file oct.top]: >> No default Proper Dih. types >> >> Please provide your suggestions. >> > > I certainly don't see how this could have happened. All the dihedral > parameters are listed explicitly. The fatal error should have printed a > line number in the .top that is problematic, so start by investigating > there. If you have modified the topology in any way, then undo the changes > and try again. > > I did not have any trouble using this .top in an unmodified form, so I > suspect you've altered it in some way that has broken it. > > -Justin > > >> >> On Mon, Mar 26, 2012 at 17:29, David van der Spoel >> wrote: >>> >>> On 2012-03-26 13:55, bipin singh wrote: >>>> >>>> Hello all, >>>> >>>> I am using the GAFF topology provided for octan-1-ol at Gromacs liquid >>>> database (http://virtualchemistry.org/molecules/111-87-5/index.php). I >>>> have incorporated all the parameters >>>> for atoms, bonds and non-bonded interaction type in the forcefield >>>> (Amber99sb-ildn in Gromacs) from GAFF topology (111-87-5.top), but I >>>> am not sure how to add the dihedraltypes information in ffbonded.itp >>>> from the GAFF topology as to add this information I need the phase and >>>> kd for each dihedral. Is this information is available in the GAFF >>>> topology provided in the Gromacs database ? >>>> >>>> >>> This topology is self supporting and you do not need anything else in >>> ffbonded.itp. >>> >>> You should be careful merging such parameters with an existing force >>> field, >>> because strictly speaking these are different force fields. >>>> >>>> >>>> >>> >>> -- >>> David van der Spoel, Ph.D., Professor of Biology >>> Dept. of Cell & Molec. Biol., Uppsala University. >>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >>> sp...@xray.bmc.uu.se http://folding.bmc.uu.se >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface >>> or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users
Re: [gmx-users] Re: How to add dihedral information from the GAFF topology
Thanks for your inputs. I have followed your suggestion and included the .itp for the octane molecule (containing atomtype definition for new atoms) in the topology file(.top) of the whole system (prot+oct+water). but during grompp it produce error and results in termination due to non matching numbers (27 atoms of octane molecule) between coordinate file and topology file. WARNING 1 [file 111-87-5.top, line 15]: Overriding atomtype h1 WARNING 2 [file 111-87-5.top, line 17]: Overriding atomtype c3 WARNING 3 [file 111-87-5.top, line 19]: Overriding atomtype ho Generated 4656 of the 4656 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 4656 of the 4656 1-4 parameter combinations Excluding 3 bonded neighbours molecule type '1-octanol' Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 3 bonded neighbours molecule type 'Ion_chain_A2' Excluding 3 bonded neighbours molecule type '1-octanol' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 55]: System has non-zero total charge: -9.89e-01 Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (box_oct_sol.gro, 54297) does not match topology (topol.top, 54324) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ##3 this is how I included the itp for the octane molecule in .top file ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" #include "octane.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Ion_chain_A2.itp" ; Include water topology #include "amber99sb-ildn.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Ion_chain_A21 1-octanol 1 SOL 565 SOL 8495 # ------- Please provide your comments. On Tue, Mar 27, 2012 at 03:20, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Thanks for your reply. >> >> Yes, you are right that these topologies are self supporting and there >> is no need to to call any other information. I followed your >> suggestions and able to generate a biphasic system of water/octane >> containing a protein molecule. But, when I tried grompp on this >> biphasic system (containing octane+water+protein), it results in error >> even if I include the topologies in forcefield.itp file. >> >> The error was >> >> Fatal error: >> Atomtype hc not found >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> > > If you introduce a new atomtype in your topology somewhere (presumably in > one of the GAFF topologies), then you have to declare them in an [atomtypes] > directive in the appropriate place in the .top file. These types are case > sensitive as well. For dealing with GAFF-type topologies, assuming you can > #include them within whatever AMBER force field you've chosen (up to you to > prove), you can do something like: > > #include "amberXX.ff/forcefield.itp" > > #include "ligand.itp" > > [ moleculetype ] > ;name nrexcl > Protein 3 > > (etc) > > The inclusion of the ligand topology (at this specific location) will add > the new [atomtypes] at the appropriate level of precedence, before any > [moleculetypes] are declared. > > > -Justin > >> On Mon, Mar 26, 2012 at 18:46, Justin A. Lemkul wrote: >>> >>> >>> bipin singh wrote: >>>> >>>> Thanks for your reply. >>>> But as far as I understood, in order to use these GAFF topology (for >>>> e.g. to perform simulation using these topologies) with Gromacs we >>>> have to incorporate the information from these topologies to the >>>> existing Amber forcefields in Gromacs or Is there anyway (Possibility >>>> of using Standalone GAFF parameters in Gromacs) to do it without >>>> performing this task. >>>> >>> As Da
Re: [gmx-users] Re: How to add dihedral information from the GAFF topology
Thanks for your suggestions. Now I am getting the following error during grompp Warning: atom name 1 in topol.top and box_prot_oct_sol.gro does not match (C1 - N) Warning: atom name 5 in topol.top and box_prot_oct_sol.gro does not match (C2 - CA) Warning: atom name 6 in topol.top and box_prot_oct_sol.gro does not match (H4 - HA) Warning: atom name 7 in topol.top and box_prot_oct_sol.gro does not match (H5 - CB) Warning: atom name 8 in topol.top and box_prot_oct_sol.gro does not match (C3 - HB1) Warning: atom name 9 in topol.top and box_prot_oct_sol.gro does not match (H6 - HB2) Warning: atom name 10 in topol.top and box_prot_oct_sol.gro does not match (H7 - OG) Warning: atom name 11 in topol.top and box_prot_oct_sol.gro does not match (C4 - HG) Warning: atom name 12 in topol.top and box_prot_oct_sol.gro does not match (H8 - C) Warning: atom name 13 in topol.top and box_prot_oct_sol.gro does not match (H9 - O) Warning: atom name 14 in topol.top and box_prot_oct_sol.gro does not match (C5 - N) Warning: atom name 15 in topol.top and box_prot_oct_sol.gro does not match (H10 - H) Warning: atom name 16 in topol.top and box_prot_oct_sol.gro does not match (H11 - CA) Warning: atom name 17 in topol.top and box_prot_oct_sol.gro does not match (C6 - HA) Warning: atom name 18 in topol.top and box_prot_oct_sol.gro does not match (H12 - CB) Warning: atom name 19 in topol.top and box_prot_oct_sol.gro does not match (H13 - HB1) Warning: atom name 20 in topol.top and box_prot_oct_sol.gro does not match (C7 - HB2) Warning: atom name 21 in topol.top and box_prot_oct_sol.gro does not match (H14 - CG) Warning: atom name 22 in topol.top and box_prot_oct_sol.gro does not match (H15 - HG) Warning: atom name 23 in topol.top and box_prot_oct_sol.gro does not match (C8 - CD1) (more than 20 non-matching atom names) WARNING 1 [file topol.top, line 55]: 28782 non-matching atom names atom names from topol.top will be used atom names from box_prot_oct_sol.gro will be ignored The order of atoms in coordinate file and order of [molecules] directive are same. I have checked on the gromacs forum and also the documentation but not able to rectify the problem. This is how I included the octane topology in .top file # ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" #include "oct.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Ion_chain_A2.itp" ; Include water topology #include "amber99sb-ildn.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Ion_chain_A21 SOL 565 1-octanol 1 SOL 8422 Please provide suggestions. On Tue, Mar 27, 2012 at 17:59, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Thanks for your inputs. >> I have followed your suggestion and included the .itp for the octane >> molecule (containing atomtype definition for new atoms) in the >> topology file(.top) of the whole system (prot+oct+water). but during >> grompp it produce error and results in termination due to non matching >> numbers (27 atoms of octane molecule) between coordinate file and >> topology file. >> >> >> >> WARNING 1 [file 111-87-5.top, line 15]: >> Overriding atomtype h1 >> >> >> WARNING 2 [file 111-87-5.top, line 17]: >> Overriding atomtype c3 >> >> >> WARNING 3 [file 111-87-5.top, line 19]: >> Overriding atomtype ho >> > > It appears that you have somehow duplicated atom types and they are > overriding each other. > > >> Generated 4656 of the 4656 non-bonded parameter combinations >> Generating 1-4 interactions: fudge = 0.5 >> Generated 4656 of the 4656 1-4 parameter combinations >> Excluding 3 bonded neighbours molecule type '1-octanol' >> Excluding 3 bonded neighbours molecule type 'Protein_chain_A' >> Excluding 3 bonded neighbours molecule type 'Ion_chain_A2' >> Excluding 3 bonded neighbours molecule type '1-octanol' >> Excluding 2 bonded neighbours molecule type 'SOL' >> Excluding 2 bonded neighbours molecule type 'SOL' >> >> NOTE 1 [file topol.top, line 55]: >> System has non-zero total charge: -9.89e-01 >> >> Program grompp, VERSION 4.5.3 >> Source code file: grompp.c, line: 523 >> >> Fatal error: >> number of coordinates in coordinate file (box_oct_sol.gro
Re: [gmx-users] Re: How to add dihedral information from the GAFF topology
Thanks for your inputs. I have checked the coordinate file thoroughly and the order of atoms are same as defined in the [molecules] directive. I really do not able to find out the source of the error. On Wed, Mar 28, 2012 at 08:55, Justin A. Lemkul wrote: > > > Biswajit Gorai wrote: >> >> Dear Bipin, >> Edit your topology file as: >> >> ### >> ; Include forcefield parameters >> #include "amber99sb-ildn.ff/forcefield.itp" >> >> ; Include chain topologies >> #include "topol_Protein_chain_A.itp" >> #include "topol_Ion_chain_A2.itp" >> >> *#include "oct.itp"* >> > > If oct.itp introduces new atom types (as the original .top does, for GAFF), > placing this topology here will result in a fatal error since there is a new > [atomtypes] directive that is introduced after the protein [moleculetype]. > If oct.itp does not introduce any new atom types, its location within the > system topology is irrelevant. > >> ; Include water topology >> #include "amber99sb-ildn.ff/tip3p.itp" >> >> #ifdef POSRES_WATER >> ; Position restraint for each water oxygen >> [ position_restraints ] >> ; i funct fcx fcy fcz >> 1 1 1000 1000 1000 >> #endif >> >> ; Include topology for ions >> #include "amber99sb-ildn.ff/ions.itp" >> >> [ system ] >> ; Name >> Protein in water >> >> [ molecules ] >> ; Compound #mols >> Protein_chain_A 1 >> Ion_chain_A2 1 >> *1-octanol 1 >> * >> *SOL 8987* > > > Depending on the order of the coordinate file, it may not be possible to > merge the SOL entries in this way. > > -Justin > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: How to add dihedral information from the GAFF topology
A lot of thanks to your "charitable mood" now the things has been resolved :) . Thanks again. On Wed, Mar 28, 2012 at 18:24, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Thanks again >> > > For the record, I didn't ask that you send me your files so I could > troubleshoot for you. Luckily for you I'm in a charitable mood this > morning, so I took a look ;) > > Your problem is that you have a [molecules] directive in oct.itp. Please > refer to the documentation for the difference between a .top topology and a > .itp topology: > > http://www.gromacs.org/Documentation/File_Formats/.itp_File > > The presence of this [molecules] directive tells grompp that the first thing > it should expect is a block of octanol, when in fact your coordinate file > has the protein first (starting with Ser-Leu, as I suspected). You then > have "1-octanol 1" in your topol.top, which says you're including another > random octanol molecule somewhere later. > > You need a single [molecules] directive in the .top, which must match the > order of the coordinate file. Once you've got that, things should work > fine. > > -Justin > > >>> From the error It seems that I have placed the octane molecule before >> >> the protein but it is not the case, I dont know why grompp is reading >> parameters for octane first and expecting it to match with protein. I >> know that its my problem and I have to think about >> that but just for the reference for you I am attaching the coordinate >> and topology files. >> >> On Wed, Mar 28, 2012 at 16:19, Justin A. Lemkul wrote: >>> >>> >>> bipin singh wrote: >>>> >>>> Thanks for your inputs. >>>> >>>> I have checked the coordinate file thoroughly and the order of atoms >>>> are same as defined in the [molecules] directive. >>>> I really do not able to find out the source of the error. >>>> >>> Looking closer at the error, what's happening is your octanol molecule is >>> in >>> a place where the topology expects the amino acid sequence Ser-Leu. >>> Perhaps >>> that will help you track down the source of the problem. It seems to me >>> that your octanol molecule occurs earlier in the coordinate file than it >>> does in the topology. >>> >>> If you still can't locate the problem, then you can always start over >>> building your system in a known order, checking the alignment of the >>> coordinate file and topology at every step. >>> >>> -Justin >>> >>> >>>> On Wed, Mar 28, 2012 at 08:55, Justin A. Lemkul wrote: >>>>> >>>>> >>>>> Biswajit Gorai wrote: >>>>>> >>>>>> Dear Bipin, >>>>>> Edit your topology file as: >>>>>> >>>>>> ### >>>>>> ; Include forcefield parameters >>>>>> #include "amber99sb-ildn.ff/forcefield.itp" >>>>>> >>>>>> ; Include chain topologies >>>>>> #include "topol_Protein_chain_A.itp" >>>>>> #include "topol_Ion_chain_A2.itp" >>>>>> >>>>>> *#include "oct.itp"* >>>>>> >>>>> If oct.itp introduces new atom types (as the original .top does, for >>>>> GAFF), >>>>> placing this topology here will result in a fatal error since there is >>>>> a >>>>> new >>>>> [atomtypes] directive that is introduced after the protein >>>>> [moleculetype]. >>>>> If oct.itp does not introduce any new atom types, its location within >>>>> the >>>>> system topology is irrelevant. >>>>> >>>>>> ; Include water topology >>>>>> #include "amber99sb-ildn.ff/tip3p.itp" >>>>>> >>>>>> #ifdef POSRES_WATER >>>>>> ; Position restraint for each water oxygen >>>>>> [ position_restraints ] >>>>>> ; i funct fcx fcy fcz >>>>>> 1 1 1000 1000 1000 >>>>>> #endif >>>>>> >>>>>> ; Include topology for ions >>>>>> #include "amber99sb-ildn.ff/ions.itp" >>>>>> >>>>>&
[gmx-users] Pressure coupling doubt
Hello, I have two doubts regarding pressure coupling in Gromacs: 1) When I use pcoupl=no the mdp.out shows the following ; Pressure coupling pcoupl = no Pcoupltype = Isotropic nstpcouple = -1 ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p= 1 compressibility = ref-p= I have not used the pcoupl(=no) then why it is showing Pcoupltype=Isotropic. (2) This is a silly question: What will happen if we use following option in mdp of NVT simulation: pcoupl=no compressibility= 4.5e-5 does it will affect the NVT criteria ? or It will ignore the compressibility input? -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Pressure coupling and Isothermal compressibility for a biphasic system
Hello All, I have some doubts regarding the use of pressure coupling and isothermal compressibility for a biphasic system (octane+water boxes built over each other). I have two questions regarding that: (1) Which pressure coupling (pcoupl) type would be suitable for this type of system ? (2) As water and octane have different compressibility, is it possible to mention the compressibility of water and octane separately? Please provide your suggestions. -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Different results from identical tpr after MD
Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. -- --- *Thanks and Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Different results from identical tpr after MD
Thanks for the reply. * *I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system (Protein/DNA/RNA) itself for a short simulation, where we don't have enough resources to run infinitely long simulation. And also how to believe the statement made by several research papers based on unconverged simulations. On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul wrote: > > > bipin singh wrote: > >> Hi all, >> >> I am really surprised to see different results from two identical md >> simulation. I have used identical tpr files for the mdrun (for 50ns) and >> after the completion of the md job I found that the results from the >> identical runs is totally different. >> >> To further confirm this, I have converted both the input tpr to mdp using >> gmxdump and diff the two files and found that the mdp is identical. >> >> Please let me know what can be the reason of this behaviour. I know that >> it is unexpected and even I can't believe how can it be possible. >> >> > It is not unexpected at all. Please consult: > > http://www.gromacs.org/**Documentation/Terminology/**Reproducibility<http://www.gromacs.org/Documentation/Terminology/Reproducibility> > > -Justin > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Different results from identical tpr after MD
Yes you are right, that we need to do multiple MD runs before making any conclusion based on single trajectory. But I have not found any single research paper which discuss about conclusions drawn based on ensemble of trajectories. If you have any such research article then please send me the link. On Thu, Apr 5, 2012 at 23:50, Peter C. Lai wrote: > Well you're really supposed to conduct multiple runs anyway. > Remember, a single MD run over a period of time only samples 1 possible > trajectory out of the ensemble of possible trajectories... > > On 2012-04-05 11:38:20PM +0530, bipin singh wrote: > > Thanks for the reply. > > * *I read the link. So, how one can predict something reliable using > these > > results(based on 50ns in my case) which changes on different machines? > > which depends more on the environment of the computer architecture and > > other variables of mdrun rather than system (Protein/DNA/RNA) itself for > a > > short simulation, where we don't have enough resources to run infinitely > > long simulation. > > And also how to believe the statement made by several research papers > based > > on unconverged simulations. > > > > On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul wrote: > > > > > > > > > > > bipin singh wrote: > > > > > >> Hi all, > > >> > > >> I am really surprised to see different results from two identical md > > >> simulation. I have used identical tpr files for the mdrun (for 50ns) > and > > >> after the completion of the md job I found that the results from the > > >> identical runs is totally different. > > >> > > >> To further confirm this, I have converted both the input tpr to mdp > using > > >> gmxdump and diff the two files and found that the mdp is identical. > > >> > > >> Please let me know what can be the reason of this behaviour. I know > that > > >> it is unexpected and even I can't believe how can it be possible. > > >> > > >> > > > It is not unexpected at all. Please consult: > > > > > > http://www.gromacs.org/**Documentation/Terminology/**Reproducibility< > http://www.gromacs.org/Documentation/Terminology/Reproducibility> > > > > > > -Justin > > > > > > -- > > > ==**== > > > > > > Justin A. Lemkul > > > Ph.D. Candidate > > > ICTAS Doctoral Scholar > > > MILES-IGERT Trainee > > > Department of Biochemistry > > > Virginia Tech > > > Blacksburg, VA > > > jalemkul[at]vt.edu | (540) 231-9080 > > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin< > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > > > > > ==**== > > > -- > > > gmx-users mailing listgmx-users@gromacs.org > > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > > Please search the archive at http://www.gromacs.org/** > > > Support/Mailing_Lists/Search< > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! > > > Please don't post (un)subscribe requests to the list. Use the www > > > interface or send it to gmx-users-requ...@gromacs.org. > > > Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > > > > > > > > > > > -- > > --- > > *Regards,* > > Bipin Singh > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > == > Peter C. Lai| University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > == > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- *Thanks and Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Different results from identical tpr after MD
Thanks for your valuable suggestions. I am totally agree with your views. On Fri, Apr 6, 2012 at 00:11, Justin A. Lemkul wrote: > > > bipin singh wrote: > >> Thanks for the reply. >> / /I read the link. So, how one can predict something reliable using >> these results(based on 50ns in my case) which changes on different >> machines? which depends more on the environment of the computer >> architecture and other variables of mdrun rather than system >> (Protein/DNA/RNA) itself for a short simulation, where we don't have enough >> resources to run infinitely long simulation. >> > > No one can do anything for an infinite amount of time ;) Hence replicate > simulations and thorough statistical analysis are required to obtain > reliable results and prove that what you've done is to be trusted. The > other comments in this thread are quite good so I won't recapitulate other > points that have been made. > > > And also how to believe the statement made by several research papers >> based on unconverged simulations. >> >> > I wouldn't trust any conclusions drawn from demonstrably unconverged > simulations. Not everything that's published has been done correctly. > Peer review is an imperfect system, so be careful what you read and apply > good scientific judgment. > > -Justin > > On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>bipin singh wrote: >> >>Hi all, >> >>I am really surprised to see different results from two >>identical md simulation. I have used identical tpr files for the >>mdrun (for 50ns) and after the completion of the md job I found >>that the results from the identical runs is totally different. >> >>To further confirm this, I have converted both the input tpr to >>mdp using gmxdump and diff the two files and found that the mdp >>is identical. >> >>Please let me know what can be the reason of this behaviour. I >>know that it is unexpected and even I can't believe how can it >>be possible. >> >> >>It is not unexpected at all. Please consult: >> >>http://www.gromacs.org/__**Documentation/Terminology/__** >> Reproducibility<http://www.gromacs.org/__Documentation/Terminology/__Reproducibility> >> >> <http://www.gromacs.org/**Documentation/Terminology/**Reproducibility<http://www.gromacs.org/Documentation/Terminology/Reproducibility> >> > >> >>-Justin >> >>-- ==**__== >> >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >>==**__== >> >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >>Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>> >> before posting! >>Please don't post (un)subscribe requests to the list. Use the www >>interface or send it to gmx-users-requ...@gromacs.org >><mailto:gmx-users-request@**gromacs.org >> >. >>Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> >> >> -- >> --- >> /Regards,/ >> Bipin Singh >> >> > -- >
Re: [gmx-users] MD after equilibration phase
Also, if we give continuation=yes in mdp file and use input as pdb file as input instead of gro file, grompp never complainsI don't no how it reads velocities from pdb file (as no velocities are present in pdb files). Ideally it should complain that no velocities found in input file On Fri, Apr 6, 2012 at 12:42, Peter C. Lai wrote: > On 2012-04-06 11:05:51AM +0400, James Starlight wrote: > > Dear Gromacs users! > > > > > > I have small question about order of the runs and input data. > > > > Ussually I do 2 equilibration phases and subsequent productive phase in > the > > conditions wich are equal to the last equilibration phase ( e.g often > this > > is npt ). > > > > In the second equil.mdp and md.mdp there is option > > > > continuation = yes > > > > which means that there have been previous phases of the simulation from > > wich coordinates and velocities should be taken. > > > > As I understood the coordinates is taken from .gro file but from what > file > > the velocities must be providen ? Does it .cpt checkpoint file from > > previous run? In some cases I've forgotten to define -t npt.cpt for my MD > > run providing only coordinates in GRO file, topology and md.mdp but I > have > > not seen any errors in such simulation due to absence of that .cpt and > > GROMPP never remind me of the absense of this file. What exactly is in > that > > .cpt file and from wich source the velocities from equilibration phase > are > > taken ? > > continuation = yes is telling LINCS that it is a continuation and > it should not attempt to refit the constrained bonds on the first pass. > > The coords, velocities, state, and box information are taken either from > the > cpt file or you can specify the previous .trr and it will take the last > frame > from that and use it. If you used the output gro file without -t, then > it will take coordinates and velocities from the .gro but the problem there > is the limited precision (3 decimal points for each). > > -- > == > Peter C. Lai| University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > == > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MD after equilibration phase
When we mention gen_vel=no ;And provide pdb as input with no velocities As mentioned in the manual: "The velocities are set to zero when there are no velocities in the input structure file" Please elaborate what does this sentence mean. On Fri, Apr 6, 2012 at 19:10, Justin A. Lemkul wrote: > > > bipin singh wrote: > >> Also, if we give continuation=yes in mdp file and use input as pdb file >> as input instead of gro file, grompp never complainsI don't no how it >> reads velocities from pdb file (as no velocities are present in pdb files). >> Ideally it should complain that no velocities found in input file >> >> > Again, the "continuation" keyword has nothing to do with velocities. If > you have "gen_vel = no" and you provide a .pdb file with no velocities, > then you do not preserve velocity information. Whatever the initial forces > are govern the resulting motions. In any case, you do not preserve the > previous simulation conditions. > > -Justin > > On Fri, Apr 6, 2012 at 12:42, Peter C. Lai > p...@uab.edu>> wrote: >> >>On 2012-04-06 11:05:51AM +0400, James Starlight wrote: >> > Dear Gromacs users! >> > >> > >> > I have small question about order of the runs and input data. >> > >> > Ussually I do 2 equilibration phases and subsequent productive >>phase in the >> > conditions wich are equal to the last equilibration phase ( e.g >>often this >> > is npt ). >> > >> > In the second equil.mdp and md.mdp there is option >> > >> > continuation = yes >> > >> > which means that there have been previous phases of the >>simulation from >> > wich coordinates and velocities should be taken. >> > >> > As I understood the coordinates is taken from .gro file but from >>what file >> > the velocities must be providen ? Does it .cpt checkpoint file from >> > previous run? In some cases I've forgotten to define -t npt.cpt >>for my MD >> > run providing only coordinates in GRO file, topology and md.mdp >>but I have >> > not seen any errors in such simulation due to absence of that >>.cpt and >> > GROMPP never remind me of the absense of this file. What exactly >>is in that >> > .cpt file and from wich source the velocities from equilibration >>phase are >> > taken ? >> >>continuation = yes is telling LINCS that it is a continuation and >>it should not attempt to refit the constrained bonds on the first pass. >> >>The coords, velocities, state, and box information are taken either >>from the >>cpt file or you can specify the previous .trr and it will take the >>last frame >>from that and use it. If you used the output gro file without -t, then >>it will take coordinates and velocities from the .gro but the >>problem there >>is the limited precision (3 decimal points for each). >> >>-- >>==**==**== >>Peter C. Lai| University of Alabama-Birmingham >>Programmer/Analyst | KAUL 752A >>Genetics, Div. of Research | 705 South 20th Street >>p...@uab.edu <mailto:p...@uab.edu> | Birmingham AL >> >>35294-4461 >>(205) 690-0808 | >>==**==**== >> >>-- >>gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>Please search the archive at >> >> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >>Please don't post (un)subscribe requests to the list. Use the >>www interface or send it to gmx-users-requ...@gromacs.org >><mailto:gmx-users-request@**gromacs.org >> >. >> >>Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> >> >> >> >> -- >> --- >> /Regards,/ >> Bipin Singh >> >> > -- > ==**==
Re: [gmx-users] MD after equilibration phase
Thanks for your comments. One more question. Does Gromacs saves velocities in pdb files, when we use gen_vel=yes option in mdp and save the output(-c) of mdrun as pdb file instead of gro file. On Fri, Apr 6, 2012 at 19:48, Mark Abraham wrote: > On 7/04/2012 12:15 AM, bipin singh wrote: > > When we mention > gen_vel=no ;And provide pdb as input with no velocities > > As mentioned in the manual: > "The velocities are set to zero when there are no velocities in the input > structure file" > > Please elaborate what does this sentence mean. > > > Each atom must have a velocity in a *dynamical* simulation. If there is no > instruction for what values to use (i.e. not generated or supplied), zero > is used. Integration proceeds from there, and this may or may not be > stable, and certainly will not have the desired temperature (yet)... > > Mark > > > > On Fri, Apr 6, 2012 at 19:10, Justin A. Lemkul wrote: > >> >> >> bipin singh wrote: >> >>> Also, if we give continuation=yes in mdp file and use input as pdb file >>> as input instead of gro file, grompp never complainsI don't no how it >>> reads velocities from pdb file (as no velocities are present in pdb files). >>> Ideally it should complain that no velocities found in input file >>> >>> >> Again, the "continuation" keyword has nothing to do with velocities. If >> you have "gen_vel = no" and you provide a .pdb file with no velocities, >> then you do not preserve velocity information. Whatever the initial forces >> are govern the resulting motions. In any case, you do not preserve the >> previous simulation conditions. >> >> -Justin >> >> On Fri, Apr 6, 2012 at 12:42, Peter C. Lai >> p...@uab.edu>> wrote: >>> >>>On 2012-04-06 11:05:51AM +0400, James Starlight wrote: >>> > Dear Gromacs users! >>> > >>> > >>> > I have small question about order of the runs and input data. >>> > >>> > Ussually I do 2 equilibration phases and subsequent productive >>>phase in the >>> > conditions wich are equal to the last equilibration phase ( e.g >>>often this >>> > is npt ). >>> > >>> > In the second equil.mdp and md.mdp there is option >>> > >>> > continuation = yes >>> > >>> > which means that there have been previous phases of the >>>simulation from >>> > wich coordinates and velocities should be taken. >>> > >>> > As I understood the coordinates is taken from .gro file but from >>>what file >>> > the velocities must be providen ? Does it .cpt checkpoint file from >>> > previous run? In some cases I've forgotten to define -t npt.cpt >>>for my MD >>> > run providing only coordinates in GRO file, topology and md.mdp >>>but I have >>> > not seen any errors in such simulation due to absence of that >>>.cpt and >>> > GROMPP never remind me of the absense of this file. What exactly >>>is in that >>> > .cpt file and from wich source the velocities from equilibration >>>phase are >>> > taken ? >>> >>>continuation = yes is telling LINCS that it is a continuation and >>>it should not attempt to refit the constrained bonds on the first >>> pass. >>> >>>The coords, velocities, state, and box information are taken either >>>from the >>>cpt file or you can specify the previous .trr and it will take the >>>last frame >>>from that and use it. If you used the output gro file without -t, then >>>it will take coordinates and velocities from the .gro but the >>>problem there >>>is the limited precision (3 decimal points for each). >>> >>>-- >>>== >>>Peter C. Lai| University of Alabama-Birmingham >>>Programmer/Analyst | KAUL 752A >>>Genetics, Div. of Research | 705 South 20th Street >>> p...@uab.edu <mailto:p...@uab.edu> | Birmingham >>> AL >>> >>>35294-4461 >>>(205) 690-0808 | >>>== >>&
Re: [gmx-users] MD after equilibration phase
Thanks for your comments I have a very crude question which may not be even logical to ask here but I just want to know your opinion on this: If I will perform two simulations in following two ways : *RUN:1* (1) Did NVT with POSRES on protein and gen_vel=yes gen_temp= 350 (2) Did NPT with POSRES on protein and continuation=yes gen_vel=no ;Without reading velocities from NVT (3) Did MD with No POSRES (NPT) continuation=yes gen_vel=no ; No velocities read from previous run * RUN:2 *(1) Did NVT with POSRES on protein and gen_vel=yes gen_temp= 350 (2) Did NPT with POSRES on protein and continuation=yes gen_vel=no ; Reading velocities from NVT run using -t option (3) Did MD with No POSRES (NPT) continuation=yes gen_vel=no ; Velocities read from previous run using -t option What will be the expected flaws of the RUN:1 over RUN:2 and will the results got from the RUN:1 is unreliable ? If yes why ? On Fri, Apr 6, 2012 at 20:26, Mark Abraham wrote: > On 7/04/2012 12:37 AM, Justin A. Lemkul wrote: > >> >> >> bipin singh wrote: >> >>> Thanks for your comments. >>> One more question. >>> Does Gromacs saves velocities in pdb files, when we use gen_vel=yes >>> option in mdp and save the output(-c) of mdrun as pdb file instead of gro >>> file. >>> >>> >> No. Velocities are only saved in the .trr and/or .cpt files. There is >> no place for velocities in .pdb files. >> > > It's conceivable that there are velocities in a mdrun -c > finalstructure.gro file, but these would have to be only at low precision, > and thus often useless. > > Mark > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding g_sham
Hello All, I have a doubt regarding -tsham option of g_sham (single histogram analysis). While using g_sham do we need to mention the temperature at which simulation were performed or it should be the constant (298.15K) for all analysis ( no matter at what temperature simulations were performed). -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding manual velocity generation in simulation
Hello All, Please let me know whether is it possible to manually assign the velocity for each atom in the simulation instead of generating through gen_vel option. -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Reference structure for PCA.
Hi vivek, I have few questions related to your query: During covariance matrix calculation, g_covar by default takes average structure of the trajectory as a reference structure then why you are giving it average structure of your trajectory (0-100ns) manually. Moreover without looking at your commands which you have used, it would be difficult for anyone that why are you getting these surprising results. On Thu, Feb 7, 2013 at 1:26 PM, vivek modi wrote: > Hello, > > I have troubled you with a similar question before also, but I guess I need > some more clarification. My question is about the reference structure in > PCA analysis. > I have 100ns long protein simulation which I want to analyze using PCA. The > RMSD shows fluctuations upto initial 25-30ns and then becomes very stable. > I have performed PCA on the last 30ns window of the simulation where I > assume the simulation has converged (I also did on other time windows as > well). > > The question is this: > I did the analysis on the last 30ns window in two ways by taking two > different reference structures. > > a. I take the average structure of the trajectory (0-100ns) as > the reference and then do the fitting and calculate covariance matrix for > last 30ns. This is done because I suspect that the average structure over > full trajectory will reflect all the changes occurring in the protein. It > also gives me low cosines (<0.1). The PCs show movement occurring in > certain regions of the protein. > > b. I take the average structure from the same window (last 30ns) then do > the fitting and calculate covariance matrix for the same. This is done with > an assumption that the reference structure must reflect the > equilibriated/stable part of the trajectory unlike the previous case. > Surprisingly it gives me high cosines (>0.5). Unlike the previous case, > this method shows very small movement in the protein (very low RMSF). > > Both of these methods give me different RMSF for the PCs although they are > done on the same part of the trajectory but the reference structure is > influencing the output. > > Which protocol among the two is appropriate ? And how can we explain high > cosines in second case where the reference structure is the average of the > same time window (there must not be large deviation) while I get low cosine > for the first case where deviations are calculated from the full trajectory > average (large deviation) ? > > Any help is appreciated. > > Thanks, > > -Vivek Modi > Graduate Student > IITK. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] MDP settings for No Temperature Coupling
Hello All, I want to know how to mention a group (group2) without any temperature coupling in mdp file. From the manual I got to know that we should mention tau_t= -1 for no temperature coupling. And in the ref_temp section I have mention two values, 300K for coupled part (group1) and 10k for uncoupled part (group2). But my doubt is while generating velocities, which temperature I should mention in gen_temp section (i.e. 300K or 10K), because as far as I know we can not mention two different temperatures in gen_temp section while generating velocities. But ideally I want the uncoupled part to be at 10K and coupled part at 300K at the starting. Please let me know, which of the below scheme is correct for this purpose: * Method:1* Tcoupl= V-rescale tau_t= 0.1 -1 tc_grps= group1 group2 ref_t= 300 10 gen_vel= yes gen_temp= 300 *Method:2* Tcoupl= V-rescale tau_t= 0.1 -1 tc_grps= group1 group2 ref_t= 300 10 gen_vel= yes gen_temp= 10 -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Difference in Number of contacts through g_hbond and g_mindist
Hi All, I have a doubt regarding the calculation of number of contacts between two groups. Because, I am getting different number of contacts calculated through g_hbond -contact option and g_mindist -on option. I have used same cutoff for distance (0.6nm) in both the cases. -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Difference in Number of contacts through g_hbond and g_mindist
Thanks for the reply. The difference is almost double, through g_hbond the average number of contacts are 1821 and through g_mindist it is 3643. The calculation group does not contains hydrogen atoms. On Mon, Mar 4, 2013 at 8:14 PM, Justin Lemkul wrote: > > > On 3/4/13 9:08 AM, bipin singh wrote: > >> Hi All, >> >> I have a doubt regarding the calculation of number of contacts between two >> groups. Because, I am getting different number of contacts calculated >> through g_hbond -contact option and g_mindist -on option. >> I have used same cutoff for distance (0.6nm) in both the cases. >> >> > How different are the results? The g_hbond code is very complex, but > you'd probably have to go into the inner workings of both programs to > understand why. I also do not know whether other settings in g_hbond will > matter, like -merge, or whether or not g_hbond will only calculate contacts > among H-bond participating groups. > > -Justin > > -- > ==**== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Difference in Number of contacts through g_hbond and g_mindist
Thanks a lot for the suggestions. It worked. On Mon, Mar 4, 2013 at 8:44 PM, Erik Marklund wrote: > As Justin implied, -merge could potentially make a factor of 2. Try > g_hbond -nomerge. > > Erik > > > On Mar 4, 2013, at 4:02 PM, bipin singh wrote: > > Thanks for the reply. >> The difference is almost double, through g_hbond the average number of >> contacts are 1821 and through g_mindist it is 3643. The calculation group >> does not contains hydrogen atoms. >> >> >> On Mon, Mar 4, 2013 at 8:14 PM, Justin Lemkul wrote: >> >> >>> >>> On 3/4/13 9:08 AM, bipin singh wrote: >>> >>> Hi All, >>>> >>>> I have a doubt regarding the calculation of number of contacts between >>>> two >>>> groups. Because, I am getting different number of contacts calculated >>>> through g_hbond -contact option and g_mindist -on option. >>>> I have used same cutoff for distance (0.6nm) in both the cases. >>>> >>>> >>>> How different are the results? The g_hbond code is very complex, but >>> you'd probably have to go into the inner workings of both programs to >>> understand why. I also do not know whether other settings in g_hbond >>> will >>> matter, like -merge, or whether or not g_hbond will only calculate >>> contacts >>> among H-bond participating groups. >>> >>> -Justin >>> >>> -- >>> ==== >>> >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> > >>> >>> ==== >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>> posting! >>> >>> * Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> >> >> >> -- >> *--- >> Thanks and Regards, >> Bipin Singh* >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use thewww > interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Free energy landscape by g_sham
g_sham calculates free energy landscapes by computing the joint probability distribution from the two dimensional plane constructed using two quantities (in your case it will be rmsd and radius of gyration). Conformations sampled during the simulation were projected on this two dimensional plane, and the number of points occupied by each cell was counted. The grid cell containing the maximum number of points is then assigned as the reference cell, with a free energy value of zero. Free energies for all the other cells were assigned with respect to this reference cell using the following equation: ΔG = -kbT ln P(x,y)/Pmin P(x,y) is the estimate of probability density function obtained from a histogram of MD data and Pmin is the maximum of the probability density function. Kb is the Boltzmann constant, and T is the temperature corresponding to each simulation. On Sun, Mar 31, 2013 at 10:35 AM, Kavyashree M wrote: > Dear users, > > > Can someone kindly explain how g_sham calculates > the free energy landscape of given two quantities say, > rmsd and radius of gyration. > Any references are welcome. > > Thank you > with Regards > Kavya > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Salt bridge Calculations
You can use g_dist with specific atoms indices to calculate distances, if you already have the information about atoms involved in salt bridge interactions. On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M wrote: > Dear users, > > Kindly clarify my doubt regarding salt bridge calculation. > > Thank you > Regards > Kavya > > > On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M wrote: > >> Dear users, >> >> For calculating salt bridge in proteins I >> am using g_hbond instead of g_saltbr. >> >> In g_hbond I use contact and mention two >> indices consisting of >> group 1: ASP_GLU_&_OD1_OD2_OE1_OE2: >> group 2: ARG_LYS_&_NZ_NE_NH1_NH2: >> >> I use the command: >> g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm >> matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5 >> >> Is this approach correct? >> >> Thank you >> Kavya >> > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RMSD from the average structure
Hi all, Please let me know whether this is the right way to calculate RMSD from the average structure from a simulation: g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg average.pdb: is the pdb file produced using -ox option of g_rmsf. -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Doubt about the Gromacs versions
Hi, Please let me know which one is the recent version of gromacs (with latest bugfixes) among the below. 4.5.7 and 4.6.1 And what is the reason behind the update for 4.5.x versions if 4.6.x versions are already available. -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RMSD from the average structure
Thanks for your reply. Actually I am interested to see how much structural deviation is occurring in a protein during the simulation from its average position of atoms rather than the initial position (crystal structure or starting structure). The motivation of doing this analysis is the fact that in real solution phase, a system may not be static and if we consider the time average structure of a simulation to be the real representative of the structure in solution phase rather than static crystal structure. On Fri, Apr 26, 2013 at 2:06 AM, Tsjerk Wassenaar wrote: > Hi Bipin Singh, > > That indeed gives you the RMSD against the average. Do think about it a bit > more: do you want the average of the whole structure, or should you account > for a phase of relaxation? > > Cheers, > > Tsjerk > > > On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul wrote: > > > > > > > On 4/24/13 3:06 AM, bipin singh wrote: > > > >> Hi all, > >> > >> Please let me know whether this is the right way to calculate RMSD from > >> the > >> average structure from a simulation: > >> > >> g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg > >> > >> > >> average.pdb: is the pdb file produced using -ox option of g_rmsf. > >> > >> > > You can calculate RMSD with respect to whatever structure you like, but > > the interpretation and justification for doing so are up to you. > > > > -Justin > > > > -- > > ==**== > > > > Justin A. Lemkul, Ph.D. > > Research Scientist > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin< > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > > > ==**== > > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > * Please search the archive at http://www.gromacs.org/** > > Support/Mailing_Lists/Search< > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! > > * Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Doubt about the Gromacs versions
Thanks for the clarification. On Thu, Apr 25, 2013 at 7:48 PM, Justin Lemkul wrote: > > > On 4/25/13 9:48 AM, Richard Broadbent wrote: > >> The 4.6.1 release is a more advanced version of gromacs with the latest >> kernels >> and features (GPU support, verlet cut-offs etc.). >> >> 4.5.7 is a maintenance release for those of us who for whatever reason >> wish to >> keep using the older 4.5.x series release. It mainly adds fixes made to >> the >> 4.6.x series to the 4.5.x version of the code. I use it as most of my >> calculations were conducted in 4.5.5 so this version allows me to use >> exactly >> the same setup as I was using before. >> >> If you are starting a new project I would suggest that the 4.6.x series >> is what >> you should use as it is substantially faster (for a system I'm running >> that >> contains no water on an Intel sandy-bridge system it is more than 50% >> faster). >> This series will also probably receive more attention in terms of bug >> fixes and >> new releases (though I'm not a developer so I could be wrong about that). >> >> > Quite right. 4.5.7 is expected to be the last version in the 4.5.x > series, and I suspect that will be true unless we discover some > catastrophic bug that needs to be patched in older versions. 4.6.x (and > the eventual transition to 5.0) will receive the greatest amount of > attention from here on out. > > -Justin > > -- > ==**== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Doubt about the Gromacs versions
Thanks for your reply. On Thu, Apr 25, 2013 at 7:18 PM, Richard Broadbent < richard.broadben...@imperial.ac.uk> wrote: > The 4.6.1 release is a more advanced version of gromacs with the latest > kernels and features (GPU support, verlet cut-offs etc.). > > 4.5.7 is a maintenance release for those of us who for whatever reason > wish to keep using the older 4.5.x series release. It mainly adds fixes > made to the 4.6.x series to the 4.5.x version of the code. I use it as most > of my calculations were conducted in 4.5.5 so this version allows me to use > exactly the same setup as I was using before. > > If you are starting a new project I would suggest that the 4.6.x series is > what you should use as it is substantially faster (for a system I'm running > that contains no water on an Intel sandy-bridge system it is more than 50% > faster). This series will also probably receive more attention in terms of > bug fixes and new releases (though I'm not a developer so I could be wrong > about that). > > Richard > > > > On 25/04/13 14:39, bipin singh wrote: > >> Hi, >> >> Please let me know which one is the recent version of gromacs (with latest >> bugfixes) among the below. >> 4.5.7 and 4.6.1 >> >> And what is the reason behind the update for 4.5.x versions if 4.6.x >> versions are already available. >> >> -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RMSD from the average structure
Dear Sir, Thanks for the useful insight. On Fri, Apr 26, 2013 at 2:21 PM, Erik Marklund wrote: > Average coordinates are problematic and not generally representative. > Consider for instance the average coordinates of a methyl group connected > to X. The rotation around the C-X bond causes the average positions of the > hydrogens to line up. Consider using g_cluster to find representative > structures from your trajectory. > > Erik > > On 26 Apr 2013, at 06:59, bipin singh wrote: > > > Thanks for your reply. > > Actually I am interested to see how much structural deviation is > occurring > > in a protein during the simulation from its average position of atoms > > rather than the initial position (crystal structure or starting > structure). > > The motivation of doing this analysis is the fact that in real solution > > phase, a system may not be static and if we consider the time average > > structure of a simulation to be the real representative of the structure > in > > solution phase rather than static crystal structure. > > > > > > > > > > > > > > > > On Fri, Apr 26, 2013 at 2:06 AM, Tsjerk Wassenaar > wrote: > > > >> Hi Bipin Singh, > >> > >> That indeed gives you the RMSD against the average. Do think about it a > bit > >> more: do you want the average of the whole structure, or should you > account > >> for a phase of relaxation? > >> > >> Cheers, > >> > >> Tsjerk > >> > >> > >> On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul wrote: > >> > >>> > >>> > >>> On 4/24/13 3:06 AM, bipin singh wrote: > >>> > >>>> Hi all, > >>>> > >>>> Please let me know whether this is the right way to calculate RMSD > from > >>>> the > >>>> average structure from a simulation: > >>>> > >>>> g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg > >>>> > >>>> > >>>> average.pdb: is the pdb file produced using -ox option of g_rmsf. > >>>> > >>>> > >>> You can calculate RMSD with respect to whatever structure you like, but > >>> the interpretation and justification for doing so are up to you. > >>> > >>> -Justin > >>> > >>> -- > >>> ==**== > >>> > >>> Justin A. Lemkul, Ph.D. > >>> Research Scientist > >>> Department of Biochemistry > >>> Virginia Tech > >>> Blacksburg, VA > >>> jalemkul[at]vt.edu | (540) 231-9080 > >>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin< > >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > >>> > >>> ==**== > >>> > >>> -- > >>> gmx-users mailing listgmx-users@gromacs.org > >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users< > >> http://lists.gromacs.org/mailman/listinfo/gmx-users> > >>> * Please search the archive at http://www.gromacs.org/** > >>> Support/Mailing_Lists/Search< > >> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! > >>> * Please don't post (un)subscribe requests to the list. Use the www > >>> interface or send it to gmx-users-requ...@gromacs.org. > >>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > >> http://www.gromacs.org/Support/Mailing_Lists> > >>> > >> > >> > >> > >> -- > >> Tsjerk A. Wassenaar, Ph.D. > >> -- > >> gmx-users mailing listgmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> * Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > > > > > > > -- > > *--- > > Thanks and Regards, > > Bipin Singh* > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Temperature for individual amino acid residues
Hi All, I want to calculate temperature for each individual amino acids residues present in a protein after the simulation. I know that this can be done with help of g_traj, but my concern is whether this will give me correct temperature or not because it was mentioned that g_traj does not mind the constraints. Please let me know what type of correction need to done on the output from g_traj if we need correct temperature values. OR Is there any way to get it from .edr file... -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Temperature for individual amino acid residues
Thanks for the reply. I have seen the link. As given in the link that we need to multiply the temperature by (3N-Ncons)/3N. Please let me know if I have correctly interpret context of the statement. "N" is the total number of protein atoms and "Ncons" will be equal to total number of constrains. 1) Do we have to take total numbers of "pairs" mentioned in .top file as a "Ncons" ( I am using all-bonds constraints in mdp file) ? 2) So, do we need to multiply by this value (single uniform number for all residues) to temperature at each step of every residue in a protein ? On Thu, May 2, 2013 at 4:56 PM, Justin Lemkul wrote: > > > On 5/2/13 1:54 AM, bipin singh wrote: > >> Hi All, >> >> I want to calculate temperature for each individual amino acids residues >> present in a protein after the simulation. I know that this can be done >> with help of g_traj, but my concern is whether this will give me correct >> temperature or not because it was mentioned that g_traj >> does not mind the constraints. Please let me know what type of correction >> need to done on the output from g_traj if we need correct temperature >> values. >> OR >> Is there any way to get it from .edr file... >> >> > http://lists.gromacs.org/**pipermail/gmx-users/2003-**March/004870.html<http://lists.gromacs.org/pipermail/gmx-users/2003-March/004870.html> > > -Justin > > -- > ==**== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Temperature for individual amino acid residues
Thanks for your reply and suggestions. On Thu, May 2, 2013 at 8:09 PM, Justin Lemkul wrote: > > > On 5/2/13 10:28 AM, bipin singh wrote: > >> Thanks for the reply. >> I have seen the link. As given in the link that we need to multiply the >> temperature by (3N-Ncons)/3N. Please let me know if I have correctly >> interpret context of the statement. "N" is the total number of protein >> atoms and "Ncons" will be equal to total number of constrains. >> > > N = number of atoms in the group being analyzed > Ncons = number of constraints in that same group > > 1) Do we have to take total numbers of "pairs" mentioned in .top file as a >> "Ncons" ( I am using all-bonds constraints in mdp file) ? >> > > Pairs have nothing to do with degrees of freedom. > > 2) So, do we need to multiply by this value (single uniform number for all >> residues) to temperature at each step of every residue in a protein ? >> >> > There is no single value; each group analyzed will have its own scaling > factor. Use of the scaling factor depends on what you want to observe, but > multiplying each frame's value by a constant and then averaging gives the > same as averaging and multiplying by a constant, so you might save yourself > some work if you just care about averages. > > -Justin > > >> >> On Thu, May 2, 2013 at 4:56 PM, Justin Lemkul wrote: >> >> >>> >>> On 5/2/13 1:54 AM, bipin singh wrote: >>> >>> Hi All, >>>> >>>> I want to calculate temperature for each individual amino acids residues >>>> present in a protein after the simulation. I know that this can be done >>>> with help of g_traj, but my concern is whether this will give me correct >>>> temperature or not because it was mentioned that g_traj >>>> does not mind the constraints. Please let me know what type of >>>> correction >>>> need to done on the output from g_traj if we need correct temperature >>>> values. >>>> OR >>>> Is there any way to get it from .edr file... >>>> >>>> >>>> http://lists.gromacs.org/pipermail/gmx-users/2003- >>> March/004870.html<http://lists.gromacs.org/**pipermail/gmx-users/2003-**March/004870.html> >>> <http://**lists.gromacs.org/pipermail/**gmx-users/2003-March/004870.** >>> html<http://lists.gromacs.org/pipermail/gmx-users/2003-March/004870.html> >>> > >>> >>> -Justin >>> >>> -- >>> ==== >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> > >>> >>> ==== >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>> posting! >>> >>> * Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> >> >> >> > -- > ==**== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding Pulling simulation:To study the base flipping of the thymine
Hi all, I am studying a system which consists of DNA duplex 20 base pairs. Actually I am interested in studying the base flipping of the thymine. I have the crystal structure of extrahelical DNA in which thymine is out side the helical structure. I want use pulling simulations to bring this base from extrahelical to Intrahelical conformation, is there any way to do it in GROMACS pull code. Please see the figure below (link) for description. http://researchweb.iiit.ac.in/~kartheek.p/extrintra.png -- Thanks and Regards, kartheek, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Segmentation fault while calculating water mediated H-bond with g_hbond
Hello all, I was trying to calculate solvent mediated H-bond between a amino acid residue (Tyr) and solvent molecule present within cutoff of 0.5nm (after creating separate index) with the help of g_hbond version 4.5.3. But I am getting segmentation fault while running g_hbond. Moreover I am getting error only for this particular residue, whereas with other residues the samilar calculation is working fine. I have used the following command for the calculation: g_hbond -f traj.xtc -s md.tpr -num hbnum.xvg -hbn hbond.ndx -g hbond.log -dist hbdist.xvg -hbm hbmap.xvg -n index.ndx Please provide your suggestions to rectify the error. -- --- *Thanks and Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Angle between two six membered rings
Hello all, I was trying to calculate the normal-normal angle between the two six membered rings using g_sgangle. I was considering the 3 atoms to define the plane for each six membered ring but I am not getting the correct values of normal-normal angle from g_sgangle in this way. Please suggest me the correct way to calculate it in gromacs . -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] fraction of native contacts calculation
Hello all, Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. *-- --- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] fraction of native contacts calculation
Thanks for your response. Hope to see this feature in upcoming GROMACS release. Before that, could it be possible to get the modified code in the user contribution section, it may be useful for many GROMACS users. On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund wrote: > > 31 okt 2012 kl. 13.43 skrev Justin Lemkul: > > > > > > > On 10/31/12 6:02 AM, bipin singh wrote: > >> Hello all, > >> > >> Is there any way to calculate fraction of native contacts during the > >> simulation in gromacs. I searched the archives but didn't found any > >> significant clue. > > > > At present, there is no way to do this. Likely one could modify the > g_mindist code to do this - it would be a very nice feature. > > > > If one could get the -sel option of g_hbond to work again then you would > get such information with -contact. > > Erik > > > > -Justin > > > > -- > > > > > > Justin A. Lemkul, Ph.D. > > Research Scientist > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > --- > Erik Marklund, PhD > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596,75124 Uppsala, Sweden > phone:+46 18 471 6688fax: +46 18 511 755 > er...@xray.bmc.uu.se > http://www2.icm.uu.se/molbio/elflab/index.html > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] fraction of native contacts calculation
Thanks for the information. On Thu, Nov 1, 2012 at 10:56 PM, Justin Lemkul wrote: > > > On 11/1/12 1:23 PM, bipin singh wrote: > >> Thanks for your response. Hope to see this feature in upcoming GROMACS >> release. Before that, could it be possible to get the modified code in the >> user contribution section, it may be useful for many GROMACS users. >> >> > If someone writes the code, certainly. Gromacs is a user-driven > community, after all :) > > If there is a feature you want, file a feature request on > redmine.gromacs.org, otherwise no one is likely to pay much attention to > it, as other, much larger changes are ongoing. > > -Justin > > > >> On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund >> wrote: >> >> >>> 31 okt 2012 kl. 13.43 skrev Justin Lemkul: >>> >>> >>>> >>>> On 10/31/12 6:02 AM, bipin singh wrote: >>>> >>>>> Hello all, >>>>> >>>>> Is there any way to calculate fraction of native contacts during the >>>>> simulation in gromacs. I searched the archives but didn't found any >>>>> significant clue. >>>>> >>>> >>>> At present, there is no way to do this. Likely one could modify the >>>> >>> g_mindist code to do this - it would be a very nice feature. >>> >>>> >>>> >>> If one could get the -sel option of g_hbond to work again then you would >>> get such information with -contact. >>> >>> Erik >>> >>> >>> -Justin >>>> >>>> -- >>>> ==**== >>>> >>>> Justin A. Lemkul, Ph.D. >>>> Research Scientist >>>> Department of Biochemistry >>>> Virginia Tech >>>> Blacksburg, VA >>>> jalemkul[at]vt.edu | (540) 231-9080 >>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>>> >>>> ==**== >>>> -- >>>> gmx-users mailing listgmx-users@gromacs.org >>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>> * Please search the archive at >>>> >>> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >>> posting! >>> >>>> * Please don't post (un)subscribe requests to the list. Use the www >>>> >>> interface or send it to gmx-users-requ...@gromacs.org. >>> >>>> * Can't post? Read >>>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>> >>> >>> --**- >>> Erik Marklund, PhD >>> Dept. of Cell and Molecular Biology, Uppsala University. >>> Husargatan 3, Box 596,75124 Uppsala, Sweden >>> phone:+46 18 471 6688fax: +46 18 511 755 >>> er...@xray.bmc.uu.se >>> http://www2.icm.uu.se/molbio/**elflab/index.html<http://www2.icm.uu.se/molbio/elflab/index.html> >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> * Please search the archive at >>> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >>> posting! >>> * Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> >>> >> >> >> > -- > ==**== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] fraction of native contacts calculation
Thanks a lot Oliver for the useful information. On Fri, Nov 2, 2012 at 12:26 AM, Oliver Beckstein wrote: > >>> Is there any way to calculate fraction of native contacts during the > >>> simulation in gromacs. I searched the archives but didn't found any > >>> significant clue. > >> > >> At present, there is no way to do this. Likely one could modify the > g_mindist code to do this - it would be a very nice feature. > >> > > > > If one could get the -sel option of g_hbond to work again then you would > get such information with -contact. > > > > In the meantime you might be able to use MDAnalysis > http://mdanalysis.googlecode.com/ and the native contact analysis in > MDAnalysis.analysis.contacts, see > http://packages.python.org/MDAnalysis/documentation_pages/analysis/contacts.html > > (If you have questions about MDAnalysis then please ask them on that > project's discussion group > http://groups.google.com/group/mdnalysis-discussion — people there are > more than happy to help.) > > Best wishes, > Oliver > > -- > Oliver Beckstein * oliver.beckst...@asu.edu > http://becksteinlab.physics.asu.edu/ > > Arizona State University > Department of Physics > Tempe, AZ 85287-1504 > USA > > Office: PSF 348 > Phone: +1 (480) 727-9765 > FAX: +1 (480) 965-4669 > > Department of Physics: > http://physics.asu.edu/home/people/faculty/oliver-beckstein > Center for Biological Physics: > http://biophysics.asu.edu/CBP/person.php?ID=343 > > > > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] fraction of native contacts calculation
Thanks a lot Sanku for your help. On Thu, Nov 1, 2012 at 11:38 PM, Sanku M wrote: > Bipin, > There might be a workaround. You might want to check out Plumed plugin > in latest versions of VMD for calculating fractions of native contact. You > can load the gromacs trajectory along with the native .gro file in VMD and > use Plumed plugin inbuilt in VMD . You need to install plumed most probably > early. > > > > ____ > From: bipin singh > To: Discussion list for GROMACS users > Sent: Thursday, November 1, 2012 1:23 PM > Subject: Re: [gmx-users] fraction of native contacts calculation > > Thanks for your response. Hope to see this feature in upcoming GROMACS > release. Before that, could it be possible to get the modified code in the > user contribution section, it may be useful for many GROMACS users. > > > On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund > wrote: > > > > > 31 okt 2012 kl. 13.43 skrev Justin Lemkul: > > > > > > > > > > > On 10/31/12 6:02 AM, bipin singh wrote: > > >> Hello all, > > >> > > >> Is there any way to calculate fraction of native contacts during the > > >> simulation in gromacs. I searched the archives but didn't found any > > >> significant clue. > > > > > > At present, there is no way to do this. Likely one could modify the > > g_mindist code to do this - it would be a very nice feature. > > > > > > > If one could get the -sel option of g_hbond to work again then you would > > get such information with -contact. > > > > Erik > > > > > > > -Justin > > > > > > -- > > > > > > > > > Justin A. Lemkul, Ph.D. > > > Research Scientist > > > Department of Biochemistry > > > Virginia Tech > > > Blacksburg, VA > > > jalemkul[at]vt.edu | (540) 231-9080 > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > > > > -- > > > gmx-users mailing listgmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > * Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to gmx-users-requ...@gromacs.org. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > --- > > Erik Marklund, PhD > > Dept. of Cell and Molecular Biology, Uppsala University. > > Husargatan 3, Box 596,75124 Uppsala, Sweden > > phone:+46 18 471 6688fax: +46 18 511 755 > > er...@xray.bmc.uu.se > > http://www2.icm.uu.se/molbio/elflab/index.html > > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > --- > *Regards,* > Bipin Singh > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Essential dynamics (ED) sampling using make_edi
Hello All, I want to use the essential dynamics (ED) sampling method to simulate the unfolding to folding process using make_edi option of GROMACS. For this task I am using -radcon option (acceptance radius contraction along the first two eigenvectors towards the folded structure (b4md.gro)) of make_edi as below: *make_edi -f eigenvec.trr -eig eigenval.xvg -s topol.tpr -tar b4md.gro -radcon 1-2 -o sam.edi * *b4md.gro:* folded structure (C-alpha only) *topol.tpr: *all atom * eigenvec.trr*:from g_covar (C-alpha only) Is this is the correct way of doing the ED sampling... Also I am not sure about the following: *1)* How to judge the correct/appropriate value for the: -maxedsteps *2)* How to judge the appropriate values for the following parameters for an Essential dynamics sampling input *(or it is neglected for ED sampling and used only for flooding input ) * -deltaF0 -deltaF -tau -alpha -T *3) *Will the output trajectory (produced using mdrun -ei sam.edi ) contain all atoms or only the C-alpha atoms (using the above make_edi command). -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] which chain to select for MD simulation
Hello, My protein have two identical chains A and B and the backbone rmsd between the two chains is 0.33A. My problem is that how to select(on what basis) one chain out of the two for md simulation, whether the selection of one of the two chains(A or B) will make any differences to the final results. -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] which chain to select for MD simulation
Sir, You are right..I exactly mean the same as you interpretednow I am clear. Thanks a lot for your reply... On Fri, Jul 8, 2011 at 13:26, felmer...@uchile.cl wrote: > Hey, > > I agree it was unclear, but i guess he meant that he has a crystal > structure with two molecules in the asymmetric unit where he knows that the > protein is a monomer in solution. Otherwise the question does not even make > sense as you pointed out. > > If it is indeed the asymmetric unit thing, then of course starting from any > of the two structures will give different resultsas they are two different > startinf points. However, on the long term all the system properties should > converge on the average. Anyways, you should obtain very similar results > from any of the two structures. > > regards > > Felipe > > Mensaje original > De: mark.abra...@anu.edu.au > Fecha: 08-jul-2011 3:44 > Para: "Discussion list for GROMACS users" > Asunto: Re: [gmx-users] which chain to select for MD simulation > > > On 8/07/2011 4:52 PM, bipin singh wrote: > > Hello, > > > > My protein have two identical chains A and B and the backbone rmsd > > between the two chains is 0.33A. > > My problem is that how to select(on what basis) one chain out of the > > two for md simulation, whether the selection of one of the two > > chains(A or B) will make any differences to the final results. > > Step back. Does it even make sense to use only one? Dimers are usually > that way for a reason. > > Mark > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Concatenating two trajectories
Hello, I want concatenate two trajectories which have same number of frames and they have written for identical time period i.e. the simulation time is same for both the trajectories(for my case 100ns each) the only thing differ is the temperature of simulation. Please suggest me whether the below commands is right for concatenating these two trajectories: trjcat -f 1.xtc 2.xtc -o concat.xtc -cat -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Concatenating two trajectories
Yes It is workingbut I have not tried that, what would be the difference if I don't give -cat option On Wed, Jul 20, 2011 at 16:16, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Hello, >> >> I want concatenate two trajectories which have same number of frames >> and they have written for identical time period i.e. the simulation >> time is same for both the trajectories(for my case 100ns each) the >> only thing differ is the temperature of simulation. >> Please suggest me whether the below commands is right for >> concatenating these two trajectories: >> >> trjcat -f 1.xtc 2.xtc -o concat.xtc -cat >> > > Presumably. Did you try it? Did it work? > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Concatenating two trajectories
Thanks Sir, I understood... On Wed, Jul 20, 2011 at 16:46, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Yes It is workingbut I have not tried that, what would be the >> difference if I don't give -cat option >> > > If the times are the same, then the second trajectory would have overwritten > the first. Please read the first paragraph of trjcat -h. > > -Justin > >> On Wed, Jul 20, 2011 at 16:16, Justin A. Lemkul wrote: >>> >>> bipin singh wrote: >>>> >>>> Hello, >>>> >>>> I want concatenate two trajectories which have same number of frames >>>> and they have written for identical time period i.e. the simulation >>>> time is same for both the trajectories(for my case 100ns each) the >>>> only thing differ is the temperature of simulation. >>>> Please suggest me whether the below commands is right for >>>> concatenating these two trajectories: >>>> >>>> trjcat -f 1.xtc 2.xtc -o concat.xtc -cat >>>> >>> Presumably. Did you try it? Did it work? >>> >>> -Justin >>> >>> -- >>> >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface >>> or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding PCA and FEL
Hello, I have constructed free energy landscape(g_sham) based on the first two principal components, can anyone suggest how to find the representative conformation for a particular region on this 2-d landscape. -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding PCA and Free energy landscape
Hello, I have constructed free energy landscape(g_sham) based on the first two principal components, can anyone suggest how to find the representative conformation for a particular region on this 2-d landscape. -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding PCA and Gibbs Free energy landscape
Hello, I have done PCA using cartesian coordinates by the help of gromacs(g_covar and g_anaeig), then using the 2-d projection of trajectory on first two eigenvectors as reaction coordinates,I have calculated a 2-d representation of the gibbs free energy landscape using gromacs.Now on this landscape I want to map the conformation(structures from the MD trajectories) of the protein onto the different region(for eg:minima)of this landscape. Please suggest how can I perform this task. -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] PCA and Free energy landscape
Hello, I have done PCA using cartesian coordinates by the help of gromacs(g_covar and g_anaeig), then using the 2-d projection of trajectory on first two eigenvectors as reaction coordinates,I have calculated a 2-d representation of the gibbs free energy landscape(g_sham) using gromacs.Now on this landscape I want to map the conformations(structures from the MD trajectories) of the protein onto the different region(for eg:minima)of this landscape. Please suggest how can I perform this task -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding g_sham
Hello, Please let me know from where can I get the full description of g_sham module, as the manual does not provide full description of the options for g_sham in gromacs. for e.g I want to know the description about the following options in g_sham: -map -ls3 -mdata -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding g_sham
Hello, Please let me know from where can I get the full description of g_sham module, as the manual does not provide full description of the options for g_sham in gromacs. for e.g I want to know the description about the following options in g_sham: -map -ls3 -mdata -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding g_sham
Thanks for yor reply... I have read manual but there is no description available for the -map -ls3 -mdata options of g_sham On Sat, Aug 13, 2011 at 15:56, lina wrote: > On Sat, Aug 13, 2011 at 3:36 PM, bipin singh wrote: >> Hello, >> Please let me know from where can I get the full description of g_sham >> module, as the manual does not >> provide full description of the options for g_sham in gromacs. >> for e.g I want to know the description about the following options in g_sham: >> >> -map >> -ls3 >> -mdata >> > > Sorry, I am not sure what's kind of "full description" you expect, > > Try: > > g_sham -h > > or > > man g_sham > >> >> >> -- >> --- >> Regards, >> Bipin Singh >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > Best Regards, > > lina > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding g_sham:Please reply
Hello, Please let me know from where can I get the full description of g_sham module, as the manual does not provide full description of the options for g_sham in gromacs. for e.g I want to know the description about the following options in g_sham: -map -ls3 -mdata -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding xpm2ps
Hello, I have xpm matrix file, for converting this file to ps format I am using xpm2ps e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label mentioned for x and y-axis, in ps file.Please let me know how to set x and y axis range label in ps file. for example I want to set the x and y-axis range from -4 to +4. -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding xpm2ps
Hello, I am using the below .m2p file as input for xpm2ps, but not able to get axis range label. ; Matrix options titlefont = Helvetica ; Matrix title Postscript Font name titlefontsize = 20.0 ; Matrix title Font size (pt) legend = yes ; Show the legend legendfont = Helvetica ; Legend name Postscript Font name legendfontsize = 12.0 ; Legend name Font size (pt) legendlabel ; Used when there is none in the .xpm legend2label; Id. when merging two xpm's xbox= 0 ; x-size of a matrix element ybox= 0 ; y-size of a matrix element matrixspacing = 20.0 ; Space between 2 matrices xoffset = 0.0 ; Between matrix and bounding box yoffset = 0.0 ; Between matrix and bounding box ; X-axis options x-lineat0value = no; Draw line at matrix value==0 x-major = 4; Major tick spacing x-minor = 2 ; Id. Minor ticks x-firstmajor= 0 ; Offset for major tick x-majorat0 = no; Additional Major tick at first frame x-majorticklen = 8.0 ; Length of major ticks x-minorticklen = 4.0 ; Id. Minor ticks x-label = ; Used when there is none in the .xpm x-font = Helvetica ; Axis label PostScript Font x-fontsize = 12; Axis label Font size (pt) x-tickfont = Helvetica ; Tick label PostScript Font x-tickfontsize = 8 ; Tick label Font size (pt) ;Y-axis options y-lineat0value = no y-major = 4 y-minor = 2 y-firstmajor= 0 y-majorat0 = no y-majorticklen = 8.0 y-minorticklen = 4.0 y-label = y-fontsize = 12 y-font = Helvetica y-tickfontsize = 8 y-tickfont = Helvetica On Wed, Aug 24, 2011 at 00:52, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Hello, >> >> I have xpm matrix file, for converting this file to ps format I am using >> xpm2ps >> e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label >> mentioned for x and y-axis, >> in ps file.Please let me know how to set x and y axis range label in ps >> file. >> for example I want to set the x and y-axis range from -4 to +4. >> >> > > Use an .m2p file: > > http://manual.gromacs.org/online/m2p.html > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding xpm2ps
Thanks for your reply, I am attaching the xpm file which I got from g_sham and also attaching the eps output got from xpm2ps.As you can see there is no axis range(PC1 and PC2) labeled in eps file. As the PC1 range is from -4 to +4 and PC2 range from -5 to +4, I want the x-axis range in eps file from -4 to +4(PC1) and y-axis range from -5 to +4(PC2) regardless of the data values in xpm file. But I am unable to get using .m2p file. On Wed, Aug 24, 2011 at 16:22, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Hello, >> I am using the below .m2p file as input for xpm2ps, but not able to >> get axis range label. >> > > What axis range do you obtain? If your data do not actually span from -4 to > 4, there's not much you can do. I was assuming you had data that did fit > this range. You also didn't say which tool produced the .xpm file; some > programs can be forced to adjust the data range, but others can't. > > -Justin > >> ; Matrix options >> titlefont = Helvetica ; Matrix title Postscript Font name >> titlefontsize = 20.0 ; Matrix title Font size (pt) >> legend = yes ; Show the legend >> legendfont = Helvetica ; Legend name Postscript Font name >> legendfontsize = 12.0 ; Legend name Font size (pt) >> legendlabel ; Used when there is none in the .xpm >> legend2label ; Id. when merging two xpm's >> xbox = 0 ; x-size of a matrix element >> ybox = 0 ; y-size of a matrix element >> matrixspacing = 20.0 ; Space between 2 matrices >> xoffset = 0.0 ; Between matrix and bounding box >> yoffset = 0.0 ; Between matrix and bounding box >> >> ; X-axis options >> x-lineat0value = no ; Draw line at matrix value==0 >> x-major = 4 ; Major tick spacing >> x-minor = 2 ; Id. Minor ticks >> x-firstmajor = 0 ; Offset for major tick >> x-majorat0 = no ; Additional Major tick at first frame >> x-majorticklen = 8.0 ; Length of major ticks >> x-minorticklen = 4.0 ; Id. Minor ticks >> x-label = ; Used when there is none in the .xpm >> x-font = Helvetica ; Axis label PostScript Font >> x-fontsize = 12 ; Axis label Font size (pt) >> x-tickfont = Helvetica ; Tick label PostScript Font >> x-tickfontsize = 8 ; Tick label Font size (pt) >> >> ;Y-axis options >> y-lineat0value = no >> y-major = 4 >> y-minor = 2 >> y-firstmajor = 0 >> y-majorat0 = no >> y-majorticklen = 8.0 >> y-minorticklen = 4.0 >> y-label = >> y-fontsize = 12 >> y-font = Helvetica >> y-tickfontsize = 8 >> y-tickfont = Helvetica >> >> On Wed, Aug 24, 2011 at 00:52, Justin A. Lemkul wrote: >>> >>> bipin singh wrote: >>>> >>>> Hello, >>>> >>>> I have xpm matrix file, for converting this file to ps format I am using >>>> xpm2ps >>>> e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label >>>> mentioned for x and y-axis, >>>> in ps file.Please let me know how to set x and y axis range label in ps >>>> file. >>>> for example I want to set the x and y-axis range from -4 to +4. >>>> >>>> >>> Use an .m2p file: >>> >>> http://manual.gromacs.org/online/m2p.html >>> >>> -Justin >>> >>> -- >>> >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface >>> or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> >
Re: [gmx-users] Regarding xpm2ps
Thanks for your kind help, I have tried as per your suggestion, the below command g_sham -f 2d_proj.xvg -xmin -5 -xmax 5 -ls gibbs.xpm It is running without any error , but it is not giving any xpm output... On Wed, Aug 24, 2011 at 17:18, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Thanks for your reply, >> I am attaching the xpm file which I got from g_sham and also attaching >> the eps output got from >> xpm2ps.As you can see there is no axis range(PC1 and PC2) labeled in eps >> file. >> As the PC1 range is from -4 to +4 and PC2 range from -5 to +4, I want >> the x-axis range in eps file from -4 to +4(PC1) >> and y-axis range from -5 to +4(PC2) regardless of the data values in xpm >> file. >> But I am unable to get using .m2p file. >> > > The .m2p file can only be used to adjust axes if the data fit the range you > want already. This was unclear from your earlier post. Now that you've > said what program you used, we can solve this. g_sham allows you to set the > axis manually with the -xmin and -xmax options. Re-run g_sham with these > options to set the axes and you should have no problem. > > -Justin > >> On Wed, Aug 24, 2011 at 16:22, Justin A. Lemkul wrote: >>> >>> bipin singh wrote: >>>> >>>> Hello, >>>> I am using the below .m2p file as input for xpm2ps, but not able to >>>> get axis range label. >>>> >>> What axis range do you obtain? If your data do not actually span from -4 >>> to >>> 4, there's not much you can do. I was assuming you had data that did fit >>> this range. You also didn't say which tool produced the .xpm file; some >>> programs can be forced to adjust the data range, but others can't. >>> >>> -Justin >>> >>>> ; Matrix options >>>> titlefont = Helvetica ; Matrix title Postscript Font name >>>> titlefontsize = 20.0 ; Matrix title Font size (pt) >>>> legend = yes ; Show the legend >>>> legendfont = Helvetica ; Legend name Postscript Font name >>>> legendfontsize = 12.0 ; Legend name Font size (pt) >>>> legendlabel ; Used when there is none in the .xpm >>>> legend2label ; Id. when merging two xpm's >>>> xbox = 0 ; x-size of a matrix element >>>> ybox = 0 ; y-size of a matrix element >>>> matrixspacing = 20.0 ; Space between 2 matrices >>>> xoffset = 0.0 ; Between matrix and bounding box >>>> yoffset = 0.0 ; Between matrix and bounding box >>>> >>>> ; X-axis options >>>> x-lineat0value = no ; Draw line at matrix value==0 >>>> x-major = 4 ; Major tick spacing >>>> x-minor = 2 ; Id. Minor ticks >>>> x-firstmajor = 0 ; Offset for major tick >>>> x-majorat0 = no ; Additional Major tick at first frame >>>> x-majorticklen = 8.0 ; Length of major ticks >>>> x-minorticklen = 4.0 ; Id. Minor ticks >>>> x-label = ; Used when there is none in the .xpm >>>> x-font = Helvetica ; Axis label PostScript Font >>>> x-fontsize = 12 ; Axis label Font size (pt) >>>> x-tickfont = Helvetica ; Tick label PostScript Font >>>> x-tickfontsize = 8 ; Tick label Font size (pt) >>>> >>>> ;Y-axis options >>>> y-lineat0value = no >>>> y-major = 4 >>>> y-minor = 2 >>>> y-firstmajor = 0 >>>> y-majorat0 = no >>>> y-majorticklen = 8.0 >>>> y-minorticklen = 4.0 >>>> y-label = >>>> y-fontsize = 12 >>>> y-font = Helvetica >>>> y-tickfontsize = 8 >>>> y-tickfont = Helvetica >>>> >>>> On Wed, Aug 24, 2011 at 00:52, Justin A. Lemkul wrote: >>>>> >>>>> bipin singh wrote: >>>>>> >>>>>> Hello, >>>>>> >>>>>> I have xpm matrix file, for converting this file to ps format I am >>>>>> using >>>>>> xpm2ps >>>>>> e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label >>>>>> mentioned for x and y-axis, >>>>>> in p
