Re: [gmx-users] number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology
On Tue, Feb 15, 2011 at 5:25 PM, Parul tew wrote: > Hi all, > first I would like to thank Justin A. Lemkul for the tutorials provided which > are very helpful for new users like me. > I am doing a membrane protein simulation and now doing packing of the lipids > around the protein. I had run the inflategro.pl script and > > and now I am facing a problem doing energy minimization of my inflated system > (contatining protein and the lipid membrane) using grompp. > I have updated my topology file accordingly ie removed the spc.itp, ions.itp > it now only contains protein and dppc > > the protein is of 3881 atoms but after updating my topolgy it still gives the > following error: > Fatal error: > number of coordinates in coordinate file (system_inflated.gro, 9331) > does not match topology (topol.top, 10281) > > As i understand it could be because of the deleted lipids of the system, if > so how can I know the deleted number of lipids. > > My topology file looks like > - > > ; > ; This is your topology file > ; protein > ; > ; Include forcefield parameters > #include "ffG53a6_lipid.itp" > > [ moleculetype ] > ; Namenrexcl > Protein_A 3 > > [ atoms ] > . > . > . > . > ; Strong position restraints for InflateGRO > #ifdef STRONG_POSRES > #include "strong_posre.itp" > #endif > > ; Include DPPC chain topology > #include "dppc.itp" > > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcxfcyfcz >11 1000 1000 1000 > #endif > > > [ system ] > ; Name > protein > 128-Lipid DPPC Bilayer > > [ molecules ] > ; Compound#mols > Protein_A 1 > DPPC128 > > After insertion, there are probably several DPPC molecules removed. Check outputs from inflategro.pl, then update accordingly. Terry > > thank you, > Parul Tewatia > > > > -- > 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] Strange behavior from g_sas
Hi, all, I have four trajectories which I want to analyze Surface on. So I run for i in 1 2 3 4; do echo -e " non-Water \n Protein " | g_sas -f $i.xtc -s $i.tpr -o $i.area.xvg -n index.ndx -q $i.pdb ; done But the strange thing is, g_sas analyzed the first three trajectories, but gave a "segmentation fault for the last one. The only difference for these trjs is the number of water molecules, hence the box size(I used NPT.) . Then I doubt maybe the atom name I used can't be put in pdb file (some of them are 5 letters long, and I used gro file since the very beginning ). I deleted the -q flag and run g_sas again, seg fault again. After searching, I did this: source /usr/local/gromacs/bin/GMXRC Then g_sas worked fine( without the -q flag). But I've already sourced GMXRC.bash. Any clue? Terry -- 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] Strange behavior from g_sas
Hi Mark, The output is like this: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. 2565 out of 4931 atoms were classified as hydrophobic Back Off! I just backed up sas/4.area.xvg to sas/#4.area.xvg.1# Back Off! I just backed up sas/4.volume.xvg to sas/#4.volume.xvg.1# There were 372 inconsistent shifts. Check your topology There were 372 inconsistent shifts. Check your topology Segmentation fault I have a periodic molecule, so there are many "inconsistent shifts" lines which I ignored before. I still don't understand why g_sas can work with the first three trjs but the last one in the same for loop. Terry On Wed, Mar 30, 2011 at 5:05 PM, Mark Abraham wrote: > On 30/03/2011 5:58 PM, Terry wrote: > >> Hi, all, >> >> I have four trajectories which I want to analyze Surface on. So I run >> >> for i in 1 2 3 4; do echo -e " non-Water \n Protein " | g_sas -f $i.xtc -s >> $i.tpr -o $i.area.xvg -n index.ndx -q $i.pdb ; done >> >> But the strange thing is, g_sas analyzed the first three trajectories, but >> gave a "segmentation fault for the last one. >> >> The only difference for these trjs is the number of water molecules, hence >> the box size(I used NPT.) . Then I doubt maybe the atom name I used can't be >> put in pdb file (some of them are 5 letters long, and I used gro file since >> the very beginning ). I deleted the -q flag and run g_sas again, seg fault >> again. >> >> After searching, I did this: >> source /usr/local/gromacs/bin/GMXRC >> Then g_sas worked fine( without the -q flag). >> >> But I've already sourced GMXRC.bash. >> > > You've either got some other installation of GROMACS that you were using, > or you changed your input files, or something about the machine changed. > Unfortunately "segmentation fault" is just a generic error. Some idea what > the output said before that might clue people in as to why that happened. > > 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
Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?
Hi Chuan, Leap is a part of Ambertools which is free. See http://ambermd.org/#AmberTools Good luck. Terry 2011/4/20 Liao Chuan > HI, Itamer and Mark, thanks for your prompt replies. > > Pymol, Amber and Sybyl are commercial software. Any free software/scripts? > > > > - Chuan > > > -- > > *发件人:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > *代表 *Mark Abraham > *发送时间:* 2011年4月20日 13:31 > *收件人:* Discussion list for GROMACS users > *主题:* Re: [gmx-users] any software which could convert a > polypeptidesequence to a pdb file? > > > > On 4/20/2011 2:36 PM, Liao Chuan wrote: > > Dear gmx-users, > > I want to conduct simulations of a protein and its ligand, a heptapeptide > HXXXPAS, where X could be tyrosine, tryptophan, pheny alanine, alanine. > Thus, I will have to conduct a total number of 4*4*4=64 runs. I’ve got the > pdb file of the protein, but I have no idea how to prepare the pdb files of > those 64 heptapeptides with sequences already known. Is there any > software/script which could convert a polypeptide sequence to a pdb file? > Any comment is appreciated! > > > Leap in the AmberTools package is good for this. > > 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
Re: [gmx-users] nodes error
Hi, You should start from here: http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm Terry On Fri, Jan 6, 2012 at 12:49 PM, Albert wrote: > Hello: > I found that each time I would like to increase my nodes for MD run, my > job always failed. it said: > > Will use 192 particle-particle and 64 PME only nodes > This is a guess, check the performance at the end of the log file > > --- > Program mdrun_mpi_bg, VERSION 4.5.5 > Source code file: ../../../src/mdlib/domdec.c, line: 6436 > > Fatal error: > There is no domain decomposition for 192 nodes that is compatible with the > given box and a minimum cell size of > 1.02425 nm > Change the number of nodes or mdrun option -rcon or -dds or your LINCS > settings > Look in the log file for details on the domain decomposition > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > > "Ohne Arbeit wird das Leben Oede" (Wir Sind Helden) > > > Does anybody have any idea for this? here is my scrips for submitting jobs; > # @ job_name = I213A > # @ class = kdm-large > # @ account_no = G07-13 > # @ error = gromacs.err > # @ output = gromacs.out > # @ environment = COPY_ALL > # @ wall_clock_limit = 12:00:00 > # @ notification = error > # @ notify_user = alb...@icm.edu.pl > # @ job_type = bluegene > # @ bg_size = 64 > # @ queue > mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args "-nosum -dlb yes -v > -s npt.tpr" -mode VN -np 256 > > > if I change the bg_size=32 and -np=128, everything goes well > > > THX > > > -- > 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
Re: [gmx-users] Re: nodes error
"The minimum cell size is controlled by the size of the largest charge group or bonded interaction and the largest of rvdw, rlist and rcoulomb, some other effects of bond constraints, and a safety margin. *Thus it is not possible to run a small simulation with large numbers of processors.*" Based on the information you provided, the only thing I can say is, MAYBE your system is "too small" to run with 256 processors. Cheers Terry On Fri, Jan 6, 2012 at 3:45 PM, Albert wrote: > thank you very much for kind reply. > > I change my command as following: > > mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_**mpi_bg -args "-nosum -dlb yes > -v -s npt.tpr -nt 1" -mode VN -np 256 > > the "-nt 1" option has been added above. but it still doesn't work and > here is the log file > > > > > Initializing Domain Decomposition on 256 nodes > Dynamic load balancing: yes > Will sort the charge groups at every domain (re)decomposition > Initial maximum inter charge-group distances: >two-body bonded interactions: 0.435 nm, LJ-14, atoms 1853 1861 > multi-body bonded interactions: 0.435 nm, Proper Dih., atoms 1853 1861 > Minimum cell size due to bonded interactions: 0.478 nm > Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nm > Estimated maximum distance required for P-LINCS: 0.819 nm > This distance will limit the DD cell size, you can override this with -rcon > Guess for relative PME load: 0.21 > > Will use 192 particle-particle and 64 PME only nodes > This is a guess, check the performance at the end of the log file > Using 64 separate PME nodes > Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 > Optimizing the DD grid for 192 cells with a minimum initial size of 1.024 > nm > The maximum allowed number of cells is: X 7 Y 7 Z 7 > > > --**- > Program mdrun_mpi_bg, VERSION 4.5.5 > Source code file: ../../../src/mdlib/domdec.c, line: 6436 > > Fatal error: > There is no domain decomposition for 192 nodes that is compatible with the > given box and a minimum cell size of > 1.02425 nm > Change the number of nodes or mdrun option -rcon or -dds or your LINCS > settings > Look in the log file for details on the domain decomposition > For more information and tips for troubleshooting, please check the GROMACS > website at > http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors> > --**- > > "It's So Fast It's Slow" (F. Black) > > > -- > 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 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] solvent group size (12548) is not a multiple of 3
On Fri, May 11, 2012 at 2:18 PM, Sangita Kachhap wrote: > > Hello all > I am runing Gromacs Tutorial KALP-15 in DPPC (I am using POPC) > I am geeting error during addiotion of ions > Fatal error: > Your solvent group size (12548) is not a multiple of 3 > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > > I have done following: > > GROMACS COMMAND > > 1) Generate topol.top using GROMOS96 53A6 parameter set > pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc > > ay prompt select 13, 2, 2 > > 2) Download: >* dppc128.pdb - the structure of a 128-lipid DPPC bilayer >* dppc.itp - the moleculetype definition for DPPC >* lipid.itp - Berger lipid parameters > > from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies > > 3) Modify topol.top with: > #include "gromos53a6.ff/forcefield.itp" > > to: > > #include "gromos53a6_lipid.ff/forcefield.itp" > > >& > > ; Include Position restraint file > #ifdef POSRES > #include "posre.itp" > #endif > > ; Include POPC chain topology > #include "popc.itp" > > ; Include water topology > #include "gromos53a6_lipid.ff/spc.itp" > > > > 4) cp files > aminoacids.rtp > aminoacids.hdb > aminoacids.c.tdb > aminoacids.n.tdb > aminoacids.r2b > aminoacids.vsd > ff_dum.itp > ffnonbonded.itp > ffbonded.itp > forcefield.itp > ions.itp > spc.itp > watermodels.dat > > from gromacs top to directory named gromos53a6_lipid.ff in working > directory. > Append parameter ([ atomtypes ], [ nonbond_params ], and [ pairtypes ])from > lipid.itp to ffnonbonded.itp & ffbonded.itp and create a forcefield.doc > file > that contains a description of the force field parameters contain > "GROMOS96 53A6 > force field, extended to include Berger lipid parameters". > Delete line ";; parameters for lipid-GROMOS interactions." and its > subsequent > line, change HW as H of [ nonbond_params ] > > > 5) Generate .tpr for POPC > grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o em.tpr -maxwarn 1 > (change OW1, HW2, HW3 to OW, HW and HW2 respectively) > > > 6) Remove periodicity > trjconv -s em.tpr -f popc128a.pdb -o popc128a_whole.gro -pbc mol -ur > compact > (at command prompt select 0) > > > 7) Oriant the KALP peptide within the same coordinate as written in end of > popc128a_whole.gro > editconf -f KALP-15_processed.gro -o KALP_newbox.gro -c -box 6.23910 > 6.17970 > 6.91950 > > > 8) Pack lipid around protein > cat KALP_newbox.gro popc128a_whole.gro > system.gro > Remove unnecessary lines (the box vectors from the KALP structure, the > header > information from the DPPC structure) and update the second line of the > coordinate file (total number of atoms) accordingly. > > > 9) Modify topol.top to add positional restrain on protein > > ; Include Position restraint file > #ifdef POSRES > #include "posre.itp" > #endif > > ; Strong position restraints for InflateGRO > #ifdef STRONG_POSRES > #include "strong_posre.itp" > #endif > > ; Include DPPC chain topology > #include "dppc.itp" > > ; Include water topology > #include "gromos53a6_lipid.ff/spc.itp" > > & > > Genrate new positional restraint > genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 > (at prompt select 2) > > Add a line "define = -DSTRONG_POSRES" to .mdp file > > > > > 10) Scale down lipid > perl inflategro.pl system.gro 0.95 POPC 0 system_shrink1.gro 5 > area_shrink1.dat > system_shrink1.gro > > > 11) addion POPC 128 to topol.top > > > 12) Solvate with water > Copy vdwradii.dat from Gromacs top to working directory and change the > value of > C from 0.15 to 0.375(to avoid addition of water in lipid hydrohphobic core) > > genbox -cp system_shrink1.gro -cs spc216.gro -o system_shrink1_solv.gro -p > topol.top > > > grompp -f ions.mdp -c system_shrink1_solv.gro -p topol.top -o ions.tpr > > genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname > CL -nn 4 > (at command prompt select 0) > Is group 0 your solvent? You should chose a group corresponding to the solvent of your system. > > > > So can anyone please help me correct this error. > > > > With regards > Sangita Kachhap > SRF > BIC,IMTECH > CHANDIGARH > > __ > सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) > Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) > सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh > पिन कोड/PIN CODE :160036 > दूरभाष/EPABX :0172 6665 201-202 > -- > 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.gro
Re: [gmx-users] problem
You should paste your topology for you metal halides so that others can help. On Fri, May 11, 2012 at 9:48 PM, Anik Sen wrote: > Hi, Am Anik Sen. AM using GROMACS 3.3.2 for one of my work. > > I was trying to run the dynamics for some inorganic metal > halides solvation in water. A fatal error is comingthat: > >- Atomtype "CH2r" not found. > > But in my system I have no such atoms. Only water molecules with tip4p > model and the inorganic metal halides. So please can anyone state whats the > problem. > > Thanking in advance > Anik Sen > > Anik Sen > Student > CSIR-Central Salt & Marine Chemicals Research Institute, > Gijubhai Badheka Marg. > Bhavnagar, Gujarat 364002 > [image: www.csmcri.org] > > > -- > 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
Re: [gmx-users] aligning problem
Check this: http://manual.gromacs.org/online/editconf.html editconf -align On Fri, Jan 25, 2013 at 1:12 PM, 申昊 wrote: > Dear GMX users, > >I have a question about aligning my molecules along specific coordinate > axis ,such as Z-axis. >Does anyone know the codes? > > > Best regards, > Hao > -- > 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
Re: [gmx-users] Using many index file in one command line
Use make_ndx to put all your groups in one .ndx file. It's totally unnecessary to use multiple .ndx file in one command. Terry On Tue, May 28, 2013 at 10:18 AM, Kieu Thu Nguyen wrote: > Dear users, > > Is there command for using many different index.ndx files in one command > line ? I used -n flag many times and gromacs report error. > > Thankful for any help! > Thu > -- > 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
Re: [gmx-users] Missing charges in a .gro file
On Mon, Sep 24, 2012 at 12:56 PM, Elie M wrote: > > Dear all, > I have created a .GRO file from a PDB file for a polymer. However in the > PDB I have positive and negative charges of some ions where as in the > produced GRO file these disappear. Are those charged atoms taken into > account in the gro file as I will be doing a MD simulation of such polymers > with nanotubes later and I dont want to work with the wrong GRO fileif > the answer is no, how do I include them? Thanks > Regards > ELie -- > http://manual.gromacs.org/online/gro.html http://manual.gromacs.org/online/top.html There are no charges in .gro files. The charges are probably discarded in your way. Terry 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
Re: [gmx-users] the CPU of REMD
The TOTAL number of cores is specified by -np option. So it's 8 in all. By the way, you can submit the job to see how. It'd be faster than waiting on the list. Terry On Thu, Oct 18, 2012 at 3:20 PM, Albert wrote: > hello: > I've got a qeustion the CPU for replica exchange. it said the REMD > should be performed by command: > > mpiexec -x -np 8 mdrun -s sd_.tpr -multi 8 -preplex 1000 > > the above command have 8 different temperature and it specify 8 cores. > Does it mean the mdrun will use 1 core (8 in all) for each subjob or 8 core > (64 in all) for each sub job? > > thank you very much. > Albert > -- > 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 * 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] how to compile double precision of 4.6?
http://www.gromacs.org/Documentation/Installation_Instructions/Cmake#double_precision_build Terry On Thu, Oct 18, 2012 at 3:07 PM, Albert wrote: > hello: > > I found with the default parameters of cmake, we can only get the single > precision gromacs 4.6. I am wondering how can we compile the double > precision? > > thank you very much > best > Albert > -- > 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 * 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] non-interactive script help
You should issue a "q" command to save and quit. So "choice.txt" should look like: ri 1-20 ... ... ri 101-120 q Cheers. Terry On Fri, Jul 22, 2011 at 1:53 PM, Chandan Choudhury wrote: > Hi gmx-users, > > I was trying to feed make_ndx with the non-interactive script, below > is my command: > > The script called "choice.txt" contained: > >> ri 1-20 > > ri 21-40 > > ri 41-60 > > ri 61-80 > > ri 81-100 > > ri 101-120 > > > Initially, I used the bash shell, then csh and tcsh, but in both the > cases it failed to produce the index_1.ndx file > > $make_ndx -f md20-80.tpr -o index_1.ndx < choice.txt > > > > Found 162 atoms with resind.+1 in range 1-20 > > 5 r_1-20 : 162 atoms > > > > Found 162 atoms with resind.+1 in range 21-40 > > 6 r_21-40 : 162 atoms > > > > Found 162 atoms with resind.+1 in range 41-60 > > 7 r_41-60 : 162 atoms > > > > Found 162 atoms with resind.+1 in range 61-80 > > 8 r_61-80 : 162 atoms > > > > Found 162 atoms with resind.+1 in range 81-100 > > 9 r_81-100: 162 atoms > > > > Found 162 atoms with resind.+1 in range 101-120 > > 10 r_101-120 : 162 atoms > > > --- > Program make_ndx, VERSION 4.5.4 > Source code file: make_ndx.c, line: 965 > > Fatal error: > Error reading user input > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > Kindly help. > > Chandan > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > -- > 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
Re: [gmx-users] how to select option for genion command automatically?
This is what you are looking for: http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts?highlight=scripting Terry On Tue, Nov 15, 2011 at 11:42 AM, Liu, Liang wrote: > I am wondering if there is a flag to make the command select SOL > automatically instead of pressing some number each time? I have thousands > of structures, it is really time-consuming to select one by one. > > -- > Best, > Liang Liu > > -- > 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
Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching.
Hi, Natalie, Obviously, number of coordinates still doesn't match the topology file even you updated the topol.top *carefully*. Check the topol.top thoroughly or paste several line of your coordinate and topology files may be good ideas. Note that the topology file is lacking information for *28* atoms. Does that number remind you anything? Terry On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson < natalie.stephen...@postgrad.manchester.ac.uk> wrote: > Hi everyone, > > I was hoping you could clear up a problem I'm having when performing energy > minimisation. I'm following the instructions from one of the tutorials > (Justin's Umbrella Sampling) with my own protein, however, this time when I > try to perform the energy minimisation it throws out this 'fatal error > message' ... > > number of coordinates in coordinate file (nrr_solv_ions.gro, 33181) > does not match topology (topol.top, 33153) > > I've been updating the topol.top file every time I've done something, so > I'm not really sure what's happened. > > Can anyone throw some light on what I've gone wrong!! > Thanks loads! > Natalie > > -- > 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
Re: [gmx-users] box size & continuing the previous energy minimization
On Fri, Dec 24, 2010 at 8:12 AM, Amit Choubey wrote: > > > On Thu, Dec 23, 2010 at 2:41 PM, mustafa bilsel wrote: > >> Hi, >> >> 1. How can I learn the box shape and size of a completed simulation? >> > > check the end of the resulting gro file . > > >> 2. I want to keep going the previous completed energy minimization by >> increasing nsteps. How can I do this? >> > > increase in nsteps, and may be the tolerance too. > > >> >> Actually, you need to start from the output .gro file, and *decrease* the "emtol" value, if your previous minimization converged. Terry > Best wishes >> Mustafa >> >> >> -- >> 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 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] dssp problem
On Fri, Dec 24, 2010 at 11:38 AM, mustafa bilsel wrote: > Hi, > I have a problem with dssp programme. > I have the programme in /home/m/DSSP. When I write > export DSSP=/usr/local/bin > and then I check /usr/local/bin I couldn't see dssp. > How can I handle this problem. I have caheceked gromacs website > > export DSSP=/path/to/dssp > > setenv DSSP /path/to/dssp > > commands are written. > Could you write export DSSP=/path/to/dssp command according to me. > > You should issue: export DSSP=/home/m/DSSP See, "/home/m/DSSP" is actually the "/path/to/dssp" in your case. Terry And also I use Ubuntu 10.04, setenv is not used, if I try to install it, I > see the package not found message. > What should I do about it? > > Best wishes > -- > 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
Re: [gmx-users] Optimization of the box size during an energy minimization?
On Fri, Dec 24, 2010 at 5:36 AM, Mark Abraham wrote: > On 24/12/2010 5:17 AM, MyLinkka wrote: > > Does anybody know if it is possible to optimize the box size during an > energy minimization in Gromacs? > > > Optimize for what criterion? > > > Can I make pressure coupling if it's possible? > > Do you mean energy minimization with pressure coupling? Terry > > Sure, that's in the manual and covered in tutorials. > > Mark > > > Is there a workaround if there is no direct way? > > Thanks! > > Ting > > > > -- > 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
Re: [gmx-users] Installation GROMACS UBUNTU
On Fri, Dec 24, 2010 at 3:45 PM, Sergio Manzetti < sergio.manze...@vestforsk.no> wrote: > Hi thanks, but if I use make it says make no Makefile found... > > Yes, Makefile should be generated by configure. You should check the last few lines that configure output to your screen and the configure log file to see what's wrong. I suggest you go to a experienced Linux user for help if you don't want to figure out how configure and make work. Terry > > > On Thu, Dec 23, 2010 at 10:46 PM, Mark Abraham wrote: > >> On 23/12/2010 9:12 PM, Sergio Manzetti wrote: >> >>> >>> >>> >>> >>> Dear Users, I am unable to get pass the first step of ./configure . This >>> step works, but when typing "make" it says: >>> >>> no targets specified and no makefile found. >>> >> >> That suggests configure did not work. >> >> >> Should it be like this, or is it compulsory to use cmake? >>> >> >> cmake is not compulsory. >> >> 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 > -- 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] grompp error! why?
2009/11/18 qing yang > Dear gmx-users, > > I am try to simulate the protein-drug, and have used drg.itp from prodrg > server2,5(beta). I have also got pro.top from pdb2gmx programs. But when I > issue a grompp command for minimization,grompp gives a fatal error. > > The error is: > > Error 0 [file "unk.itp",line 4] > > Not enough parameters > > ….. > > Fatal error: > > Bonded/nonbonded atom type '1' not found! > > My pro.top file: > >#include “ffg43a1.itp” > > Did you input this line with keyboard? Try #include "ffG43a1.itp" Terry #include “unk.itp” > >[molecules] > >Protein1 > >UNK 1 > >SOL 109324 > > My drg.itp file: > > [ atoms ] > ; nr type resnr resid atom cgnr charge mass > 1 CR1 1 UNK CBF 10.003 12.0110 > 2HC 1 UNK HBF 10.035 1.0080 >... > [ bonds ] > ; ai aj fuc0, c1, ... >1 2 20.109 1230.00.109 1230.0 ; CBF HBF >1 3 20.139 1080.00.139 1080.0 ; CBF CBG > . > [ pairs ] > ; ai aj fuc0, c1, ... >1 6 1 ; CBF NBK >1 9 1 ; CBF CBI >. > [ angles ] > ; ai aj ak fuc0, c1, ... >2 1 3 2120.0 505.0120.0 505.0 ; > HBF CBF CBG >2 1 13 2120.0 505.0120.0 505.0 ; > HBF CBF CBE > > [ dihedrals ] > ; ai aj ak al fuc0, c1, m, ... > 1 13 3 2 2 0.0 167.40.0 167.4 ; imp > CBF CBE CBG HBF > 3 1 5 4 2 0.0 167.40.0 167.4 ; imp > CBG CBF CBH HBG > Maybe someone knows what the problem might be?How can I deal with this > problem? > Thanks for your help! > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] amber force field in gromacs
Hi Leila, I think it is a pdb format problem. According to pdb convention, column 17 should be left blank and columns 18-20 are used for residue name. Please check your pdb format first. Good luck. Terry 2009/11/21 leila karami > Hi > > I used amber03 force field in gromacs to study pr-dna interaction. > I compare my pdb file and ffamber03.rtp file. > I should correct my pdb file to tally with rtp file. N-terminal (NUMBER 1) > and C-terminal (NUMBER 70) of my protein is GLY. > pdb file and rtp file relating to gly1 and gly70 are placed in follow. > > pdb file of gly1: > > 1 N NGLY 1 > 2 CA NGLY 1 > 3 C NGLY 1 > 4 O NGLY 1 > 5 1H NGLY 1 > 6 2HA NGLY 1 > 7 2H NGLY 1 > 8 3H NGLY 1 > 9 1HA NGLY 1 > > rtp file of gly1: > > [ NGLY ] > [ atoms ] > Namber99_39 0.29430 1 > H1amber99_17 0.16420 2 > H2amber99_17 0.16420 3 > H3amber99_17 0.16420 4 > CAamber99_11 -0.01000 5 >HA1amber99_28 0.08950 6 >HA2amber99_28 0.08950 7 > Camber99_20.61630 8 > Oamber99_41 -0.57220 9 > > pdb file of gly70: > > 1 N CGLY A 70 > 2 CA CGLY A 70 > 3 C CGLY A 70 > 4 O CGLY A 70 > 5 H CGLY A 70 > 6 2HA CGLY A 70 > 7 1HA CGLY A 70 > 8 OXT CGLY A 70 > 9 CGLY A 70 > > rtp file of gly70: > > [ CGLY ] > [ atoms ] > Namber99_34 -0.38210 1 > Hamber99_17 0.26810 2 > CAamber99_11 -0.24930 3 >HA1amber99_19 0.10560 4 >HA2amber99_19 0.10560 5 > Camber99_20.72310 6 >OC1amber99_45 -0.78550 7 >OC2amber99_45 -0.78550 8 > before correction of pdb file, following warning and error was came up: > > *WARNING: atom H is missing in residue GLY 1 in the pdb file > You might need to add atom H to the hydrogen database of residue > GLY > in the file ff???.hdb (see the manual) > * > *Fatal error: > There were 1 missing atoms in molecule Protein_A, if you want to use this > incomplete topology anyhow, use the option -missing > * > ffamber03.hdb: > * * > NGLY 2 > 3 4 HN CA C > 2 6 HA CA N C > > I didn't use -missing option. > > please guide me. > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] amber force field in gromacs
Hi, Sorry for my mistake before, column 17 should be alternative location code, not blank. Good luck Terry 2009/11/21 leila karami > Hi > > I used amber03 force field in gromacs to study pr-dna interaction. > I compare my pdb file and ffamber03.rtp file. > I should correct my pdb file to tally with rtp file. N-terminal (NUMBER 1) > and C-terminal (NUMBER 70) of my protein is GLY. > pdb file and rtp file relating to gly1 and gly70 are placed in follow. > > pdb file of gly1: > > 1 N NGLY 1 > 2 CA NGLY 1 > 3 C NGLY 1 > 4 O NGLY 1 > 5 1H NGLY 1 > 6 2HA NGLY 1 > 7 2H NGLY 1 > 8 3H NGLY 1 > 9 1HA NGLY 1 > > rtp file of gly1: > > [ NGLY ] > [ atoms ] > Namber99_39 0.29430 1 > H1amber99_17 0.16420 2 > H2amber99_17 0.16420 3 > H3amber99_17 0.16420 4 > CAamber99_11 -0.01000 5 >HA1amber99_28 0.08950 6 >HA2amber99_28 0.08950 7 > Camber99_20.61630 8 > Oamber99_41 -0.57220 9 > > pdb file of gly70: > > 1 N CGLY A 70 > 2 CA CGLY A 70 > 3 C CGLY A 70 > 4 O CGLY A 70 > 5 H CGLY A 70 > 6 2HA CGLY A 70 > 7 1HA CGLY A 70 > 8 OXT CGLY A 70 > 9 CGLY A 70 > > rtp file of gly70: > > [ CGLY ] > [ atoms ] > Namber99_34 -0.38210 1 > Hamber99_17 0.26810 2 > CAamber99_11 -0.24930 3 >HA1amber99_19 0.10560 4 >HA2amber99_19 0.10560 5 > Camber99_20.72310 6 >OC1amber99_45 -0.78550 7 >OC2amber99_45 -0.78550 8 > before correction of pdb file, following warning and error was came up: > > *WARNING: atom H is missing in residue GLY 1 in the pdb file > You might need to add atom H to the hydrogen database of residue > GLY > in the file ff???.hdb (see the manual) > * > *Fatal error: > There were 1 missing atoms in molecule Protein_A, if you want to use this > incomplete topology anyhow, use the option -missing > * > ffamber03.hdb: > * * > NGLY 2 > 3 4 HN CA C > 2 6 HA CA N C > > I didn't use -missing option. > > please guide me. > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] No K+ for ffG53a6 ?
Hi all, I am new to gmx. I want to use potassium ions in my system. But grompp gives me only error. So I go through ffG53a6.atp, but find no atom type for potassium. Is this normal or I made some mistakes? If this is normal, how can I use potassium ion with ffG53a6? Thanks Terry -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Amber port for GROMACS 4.0
Hi All, I was wondering how I can aquire AMBER ports for GROMACS4.0? Considering the ports given in (http://chemistry.csulb.edu/ffamber/) are suitable for version 3.3.3 and older. Noting the FAQ (http://chemistry.csulb.edu/ffamber/FAQ.html): - Can I use these ports with any version of GROMACS? No! The ports are numbered to coincide with GROMACS releases, and minor differences between GROMACS versions render the ports non-interchangable. -- Cheers, Terry ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] range of magnitude for force constant
Hi, I have rather elementary questions regarding force constants used in restraining position/orientation: - I have imposed a force with constants kx, ky, and kz =10^6 kJ/mol/nm^2 on a particular atom of a peptide to harmonically position restrain the molecule inside a bilayer. Is it alright to use such high values for force constants? I have used kz =10^3 kJ/mol/nm^2 but it seems that the peptide can still move 2-3 angstrom up and down during the course of 200ps simulation so I needed to restrain it more tightly. - If I calculate PMF along the z-coordinate (performing separate MD's for the peptide along z axis) -- assuming i get reasonable overlaps for the histograms -- would such a large number create (numerical) problems in WHAM calculations? - what is a typical force constant to use in angle_restraint_z (referring to formula 4.68 in 3.3 manual). Considering the units of k_c, is 500kJ/mol way off? -- Cheers, Terry ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] [ angle_restraints_z ]
Hi all, There are atoms (a1 and a2) in my small molecule coordinate file that have the same z component: a1: atom#22 (x1,y1,60.231) a2: atom#45 (x2,y2,60.231)If I use these lines only Therefore the vector a1-a2 makes theta=90o with the z-axis. in my previous MD runs the a1-a2 were flexible (theta was observed in the range of 30-120 degrees). To restrain a1-a2 at this orientation throughout my MD calculations I included these lines to my starting topology: ; Restrain the molecules wrt z-axis... [ angle_restraints_z ] ; #1 #2 typetheta0(degrees) k_c(kJ mpl^(-1)) multiplicity 22 45 1 90 10001 Would someone comment on: - Is this is all I need to do to restrain a1-12 wrt z-axis? - Are the above parameters (theta/K/multiplicity) reasonable/correct? - with this I should expect a1 and a2 stay in xy-plane (with their z component equal at each frame) during minimization, equilibration and production? Thanks. -- Cheers, Terry ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] [ angle_restraints_z ]
Dear Berk, Thanks for the reply. Yes. In fact I made the choice of multiplicity=1 based on the explanation in eq. 4.68: "A multiplicity (n) of 2 is useful when you do not want to distinguish between parallel and anti-parallel vectors." Since my molecule is slightly polar and it may matter whether it is at 0 or 180 orientation, I decided to use multiplicity of 1. Please correct me if I am missing something. If multiplicity 1 is OK do you still think that the force constant 1000 kJ/mo is too large in my system? On Mon, May 19, 2008 at 5:34 PM, Berk Hess <[EMAIL PROTECTED]> wrote: > > > > > -- > Date: Sat, 17 May 2008 08:48:28 +0330 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] [ angle_restraints_z ] > > > Hi all, > > There are atoms (a1 and a2) in my small molecule coordinate file that have > the same z component: > a1: atom#22 (x1,y1,60.231) > a2: atom#45 (x2,y2,60.231)If I use these lines only > > Therefore the vector a1-a2 makes theta=90o with the z-axis. in my previous > MD runs the a1-a2 were flexible (theta was observed in the range of 30-120 > degrees). > To restrain a1-a2 at this orientation throughout my MD calculations I > included these lines to my starting topology: > > ; Restrain the molecules wrt z-axis... > [ angle_restraints_z ] > ; #1 #2 typetheta0(degrees) k_c(kJ mpl^(-1)) multiplicity > 22 45 1 90 10001 > > Would someone comment on: > - Is this is all I need to do to restrain a1-12 wrt z-axis? > - Are the above parameters (theta/K/multiplicity) reasonable/correct? > - with this I should expect a1 and a2 stay in xy-plane (with their z > component equal at each frame) during minimization, equilibration and > production? > > Thanks. > > -- > Cheers, > Terry > > > Did you look at formula 4.68 in the manual? > What you want is a minimum at 90 and maxima at 0 and 180. > So you need to use a multiplicity of 2. > 1000 as a force constant seems too large to me, this means that > the 0/180 degrees is penalized by 2000 kJ/mol. > > Berk. > > > -- > Express yourself instantly with MSN Messenger! MSN > Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Cheers, Terry ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] which tpr?
Hello all, Because of the limitations in run time, my simulations have broken into three parts: one.trr, two.trr, and three.trr. Each run has its corresponding tpr file. The original tpr file (minimization step) was start.tpr. Now using trjconv for three.trr which tpr file I need to type after -s option? trjconv -f three.trr -s start.tpr I am aware that the topology (information in the starting top file) will remain intact during simulation. I am wondering whether commands like trjconv read anything more than topology information (MD parameters, etc) from the -s option? In other words, in the above example replacing start.tprwith three.tpr will not change the outcome? Cheers, Terry ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] viewing .xvg plots in windows environment
Hi, I am trying to view my GROMACS ".xvg" outputs (2D plots) in windows XP environment. Can anyone please suggest a good way to do this? -- Cheers, Terry ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
