[gmx-users] Re: gmx-users Digest, Vol 93, Issue 72
Dear All, Could anybody tell me how to take the coordinates of the first and second solvation shell with solute from the snapshots of MDS run. Which molecular viewer will be good for it. Thank you *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- 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 Molecular Viewer
Dear All, > Could anybody tell me how to take the coordinates of the > first and second solvation shell with solute from the snapshots of MDS run. > Which molecular viewer will be good for it. > > Thank you > > *With Regards, > Ravi Kumar Venkatraman, > IPC Dept., IISc, > Bangalore, INDIA. > > +91-9686933963.* > -- 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] constrained mdrun about linear rigid molecule ??
Hi, I'm not good at handling Gromacs yet. My question is about virtual interaction. I'm doing simulation dealing with CO2 which is linear rigid molecule as you already know. As pervasively known, I introduced virtual sites. However, I don't know how to give initial coordinate correctly of dummy particles. Let us consider following system. x1-d1-x2 There are two real atom and one dummy particle between them with appropriate length ratio, a, from x1, and (1-a) from x2. If I give the coordinates of three particles by the rules of above statement, i.e., dummy particle between them with appropriate length ratio, a, from x1, and (1-a) from x2.. Is it correct? Isn't there any unstable energy? Do I have to run any preceding run before equilibration run?? Otherwise, Is there any other way giving the correct coordinate of dummy particle ??? Please help 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/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] Protein angles / single point calculations
Hi, I have some questions. First, what dihedral angles will Gromacs produce and use in topology when simulating proteins? To be more specific, I was looking for psi (N-C(a)-C-N) and phi (C-N-C(a)-C) angles in all the dihedrals that were generated by pdb2gmx. I only found the psi angles but not phi. Is that by purpose? Second, for testing purposes, I want to do single point energy calculations in vacuo with no cutoffs at given coordinates. When I use an mdp like the one below, it always changes the coordinates slightly but enough to change the energy values noticeably. Is there a better way to to this? Third, I'm not sure if the coordinates are used correctly. To compare the energy values, I inserted a little piece of code in the energy evaluation routines which outputs the coordinates of all atoms. It seems that everything beyond the three digits after the decimal sign in the .gro files is filled with arbitrary numbers. I know that using floating point data types results in a loss of accuracy but I thought even with single precision, the accuracy should be higher than three digits? Here is my mdp: constraints = all-bonds integrator= MD nsteps = 0 nstcomm = 1 ns_type= grid rlist = 0.0 rcoulomb = 0.0 rvdw= 0.0 Tcoupl = no Pcoupl = no gen_vel= no pbc = no I would greatly appreciate any help and comments. Best regards, Matthias Ernst -- 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] Protein angles / single point calculations
On 12/01/2012 9:14 PM, Matthias Ernst wrote: Hi, I have some questions. First, what dihedral angles will Gromacs produce and use in topology when simulating proteins? To be more specific, I was looking for psi (N-C(a)-C-N) and phi (C-N-C(a)-C) angles in all the dihedrals that were generated by pdb2gmx. I only found the psi angles but not phi. Is that by purpose? If your force field doesn't implement such dihedrals, then they won't be there. However it seems to me more likely that you aren't looking in enough right places. Consider the opposite order of the atom numbers, also. Second, for testing purposes, I want to do single point energy calculations in vacuo with no cutoffs at given coordinates. When I use an mdp like the one below, it always changes the coordinates slightly but enough to change the energy values noticeably. Is there a better way to to this? Zero-step MD is a way to do this. Using constraints = none, or continuation = yes will stop slight changes from the use of constraints. Another alternative is using mdrun -rerun, which is efficient for doing many such evaluations, and guarantees no changes to the coordinates. Third, I'm not sure if the coordinates are used correctly. To compare the energy values, I inserted a little piece of code in the energy evaluation routines which outputs the coordinates of all atoms. It seems that everything beyond the three digits after the decimal sign in the .gro files is filled with arbitrary numbers. I know that using floating point data types results in a loss of accuracy but I thought even with single precision, the accuracy should be higher than three digits? The accuracy is as high as it can be - I think you're assuming nothing has happened, and that isn't quite true. Mark Here is my mdp: constraints = all-bonds integrator= MD nsteps = 0 nstcomm = 1 ns_type= grid rlist = 0.0 rcoulomb = 0.0 rvdw= 0.0 Tcoupl = no Pcoupl = no gen_vel= no pbc = no I would greatly appreciate any help and comments. Best regards, Matthias Ernst -- 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] PRODRG charges
Hi Many thanks for your reply and sorry to come back on this. Is the fitting to experimental free energies of solvation, the only acceptable way to get "GROMOS-compatible charges"? Acceptable because this is the way that partial charges were derived for the gromos ff. In the quite usual case that these experimental data are not available for the ligand one is interested in, are DFT/ESP charges acceptable? Thanks again. George > > > g...@bioacademy.gr wrote: >> Hello >> >> Given that the partial charges from PRODRG are not reliable (as >> explained >> Justin Lemkul's paper), >> are AM1-BCC charges calculated with the Chimera/Amber Tools a reasonable >> starting point? >> > > Yes, those charges are a reasonable start, but will almost certainly not > be > sufficient for the final topology. > >> In this case, do we treat all ligand atoms as one charge group? >> > > Unless your ligand is 4 atoms or less, no. Please consult the manual > regarding > charge groups, and see existing Gromos96 building blocks for suitable > charge > groupings. > > -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 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] PRODRG charges
On 2012-01-12 12:42, g...@bioacademy.gr wrote: Hi Many thanks for your reply and sorry to come back on this. Is the fitting to experimental free energies of solvation, the only acceptable way to get "GROMOS-compatible charges"? Acceptable because this is the way that partial charges were derived for the gromos ff. In the quite usual case that these experimental data are not available for the ligand one is interested in, are DFT/ESP charges acceptable? No. CHeck http://compbio.biosci.uq.edu.au/atb/ Thanks again. George g...@bioacademy.gr wrote: Hello Given that the partial charges from PRODRG are not reliable (as explained Justin Lemkul's paper), are AM1-BCC charges calculated with the Chimera/Amber Tools a reasonable starting point? Yes, those charges are a reasonable start, but will almost certainly not be sufficient for the final topology. In this case, do we treat all ligand atoms as one charge group? Unless your ligand is 4 atoms or less, no. Please consult the manual regarding charge groups, and see existing Gromos96 building blocks for suitable charge groupings. -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 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 -- 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.sehttp://folding.bmc.uu.se -- 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] PRODRG charges
On 12/01/2012 10:42 PM, g...@bioacademy.gr wrote: Hi Many thanks for your reply and sorry to come back on this. Is the fitting to experimental free energies of solvation, the only acceptable way to get "GROMOS-compatible charges"? Acceptable because this is the way that partial charges were derived for the gromos ff. In the quite usual case that these experimental data are not available for the ligand one is interested in, are DFT/ESP charges acceptable? Possibly, but you'd have a higher burden of proof that your simulation is a valid model of reality then if the parametrization was consistent. This trade-off could well drive the choice of a different force field. Mark Thanks again. George g...@bioacademy.gr wrote: Hello Given that the partial charges from PRODRG are not reliable (as explained Justin Lemkul's paper), are AM1-BCC charges calculated with the Chimera/Amber Tools a reasonable starting point? Yes, those charges are a reasonable start, but will almost certainly not be sufficient for the final topology. In this case, do we treat all ligand atoms as one charge group? Unless your ligand is 4 atoms or less, no. Please consult the manual regarding charge groups, and see existing Gromos96 building blocks for suitable charge groupings. -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 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] Problem with FE-Cys covalent bond
Hi: Did you add the parameters for the new covalent bond to the correct part of ffbonded.itp? Because, for the GROMOS FF you have to add the parameters for the new bond, angle and dihedral ,created due to specbond, in a certain part of the ffbonded.itp for pdb2gmx be able to use it. I dont know if the OPLS FF function in the same way but probably will be something trivial like these. Take a look at the bottom part of the ffbonded.itp in one of the GROMOS FF for example gromos53a5.ff. Best Regards, Anthony On Wed, Jan 11, 2012 at 6:34 AM, Mark Abraham wrote: > On 11/01/2012 7:14 PM, Suman Nandy wrote: >> >> Dear gromacs users, >> >> I have a problem regarding the simulation of Fe4S4 cluster attached to CYS >> of a protein using opls ff. I editted the "aminoacids.rtp" file as like >> this. >> >> [ SF4 ] >> ... [ atoms ] >> FE1 opls_966 2.500 1 >> FE2 opls_967 2.500 1 >> FE3 opls_968 2.500 1 >> FE4 opls_969 2.500 1 >> S1 opls_970 -2.000 1 >> S2 opls_971 -2.000 1 >> S3 opls_972 -2.000 1 >> S4 opls_973 -2.000 1 >> [ bonds ] >> FE1 S1 >> FE1 S2 >> FE1 S3 >> FE2 S1 >> FE2 S2 >> FE2 S4 >> FE3 S2 >> FE3 S3 >> FE3 S4 >> FE4 S1 >> FE4 S2 >> FE4 S3 >> >> and also "atomtypes.atp" as >> >> opls_966 55.84500 ; FE1: HEME >> opls_967 55.84500 ; FE2: HEME >> opls_968 55.84500 ; FE3: HEME >> opls_969 55.84500 ; FE4: HEME >> opls_970 32.06000 ; S1: S >> opls_971 32.06000 ; S2: S >> opls_972 32.06000 ; S3: S >> opls_973 32.06000 ; S4: S >> >> I have also added a line to "specbond.dat" regarding the SG-FE covalent >> bond. But while running the pdb2gmx command, (withouit any error) it just >> adds a H with SG (where the FE to bind)and there is no information on SG-FE >> bond in topology file. Please help. > > > You should inspect the output of pdb2gmx to see what it thinks about the > sulfur cluster. It's either not close enough or not considered part of the > same [moleculetype] being created. You may need to choose PDB chain IDs and > pdb2gmx -chainsep more suitably. > > 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 -- 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] problem with gromacs
Hello, Thanks for your advice. I use "make distclean" before configure. But an error appeared in the same place. cd gromacs-4.5.5 make distclean ./configure --disable-threads make .libs/xlate.o:xlate.c:(.text+0xa9b): undefined reference to `_put_symtab' .libs/xlate.o:xlate.c:(.text+0xb3a): undefined reference to `_save_free' .libs/xlate.o:xlate.c:(.text+0xba6): undefined reference to `_save_free' .libs/xlate.o:xlate.c:(.text+0xc0d): undefined reference to `_save_free' .libs/xlate.o:xlate.c:(.text+0xc6d): undefined reference to `_save_free' .libs/xlate.o:xlate.c:(.text+0xc99): undefined reference to `_save_free' collect2: ld returned 1 exit status Makefile:459: recipe for target `libgmxpreprocess.la' failed make[3]: *** [libgmxpreprocess.la] Error 1 make[3]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src/kernel' Makefile:302: recipe for target `all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src' Makefile:238: recipe for target `all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src' Makefile:347: recipe for target `all-recursive' failed make: *** [all-recursive] Error 1 And what should I do, now? Sylwia Chmielewska -- 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] constrained mdrun about linear rigid molecule ??
On 12/01/2012 8:40 PM, Kiwoong Kim wrote: Hi, I'm not good at handling Gromacs yet. My question is about virtual interaction. I'm doing simulation dealing with CO2 which is linear rigid molecule as you already know. As pervasively known, I introduced virtual sites. However, I don't know how to give initial coordinate correctly of dummy particles. Let us consider following system. x1-d1-x2 There are two real atom and one dummy particle between them with appropriate length ratio, a, from x1, and (1-a) from x2. If I give the coordinates of three particles by the rules of above statement, i.e., dummy particle between them with appropriate length ratio, a, from x1, and (1-a) from x2.. Is it correct? Looks fine. Isn't there any unstable energy? Why should there be? Do I have to run any preceding run before equilibration run?? Otherwise, Is there any other way giving the correct coordinate of dummy particle ??? I expect you can give it any coordinates you like, and the interaction any value of a you like. Thereafter, it's in the hands of physics. If you want something reasonable, then probably choose the coordinates and the value of a in a consistent way. 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] Pull code problem: Large fluctuations in pull force in Gromacs 4.5.1 compared to 4.0.5
Dear all, I have a problem using the pull code in Gromacs 4.5.1. I am running simulations with a small molecule at constrained distances from the bilayer center in a membrane (z-direction) in order to calculate permeability data. I use the force acting on the molecule (pullf.xvg) at different distances to calculate free energy profiles and diffusion coefficients. The problem I am facing is that the pull forces are fluctuating significantly more in version 4.5.1 compared to in 4.0.5. In 4.0.5 the forces normally fluctuate in the range of at most ±2000 kJ/mol/nm whereas in 4.5.1 they fluctuate in the range of at most ±5 kJ/mol/nm. The average force is however similar in both versions, which results in reasonable calculated free energy profiles. However, the large fluctuations in forces make the autocorrelation function of the force different, and this causes problems when calculating diffusion coefficients. I have used the same mdp file as in version 4.0.5 with the difference that tau_t is increased from 0.1 to 0.4 (mdp file included below). The simulations are at least 7 ns. Is there anything trivial that I have missed when changing from version 4.0.5 to 4.5.1? I would really appreciate any help on this issue. Thanks in advance. Regards, Emma The mdp file: title= x cpp = /lib/cpp include = define = integrator= md dt= 0.002 nsteps = 750 nstlog= 25000 nstenergy= 30 nstxout= 0 nstxtcout = 25000 nstvout= 0 nstfout = 0 xtc_grps = DPPC SOL X energygrps = DPPC SOL X nstlist= 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.0 tcoupl = Nose-hoover tc-grps = DPPC SOL X tau_t= 0.4 0.4 0.4 ref_t = 323 323 323 Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p= 1.0 1.0 compressibility = 4.5e-5 4.5e-5 ref_p= 1.0 1.0 gen_vel= yes gen_temp = 323 gen_seed= 173529 constraints = all-bonds pbc = xyz optimize_fft = yes unconstrained_start = no pull = constraint pull_geometry = cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0= DPPC pull_group1= X pull_vec1 = 0 0 1 pull_init1 = -0.006 -- 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] optimum acceptance ratio for REMD
Hi all, I am currently puzzled by the emphasis on using an acceptance ratio of around 0.2 for replica exchange simulations in the literature. This optimum ratio is, as far as I understand, derived assuming that the exchange attempt frequency is constant and that the protein dynamics are not limiting the diffusion of a replica up and down the temperature ladder. In a real system there will be some time-scale associated with the relaxation of the protein as it moves from one temperature to another. The rate of diffusion of the replica on the temperature ladder could potentially be limited by these protein dynamics or by the exchange frequency. If we are limited by the exchange frequency, then it would make sense to decrease the interval between exchange attempts to the same time-scale as the potential energy correlation time, and to choose the number of replicas such that the acceptance ratio was around 0.2. If we are limited by the protein dynamics then the exchange frequency doesn't matter, so the acceptance ratio should have no effect (as long, of course, as it isn't so low that the exchange frequency becomes limiting). This would mean for simulations of large proteins where the protein dynamics are limiting, we can slash the number of replicas required for an efficient REMD simulation. However, I haven't seen any simulations in the literature using very small acceptance ratios, which makes me suspicious of my logic. Does anyone have any thoughts on this? Cheers, Ben -- 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] optimum acceptance ratio for REMD
On 2012-01-12 19:42, Ben Reynwar wrote: Hi all, I am currently puzzled by the emphasis on using an acceptance ratio of around 0.2 for replica exchange simulations in the literature. This is bogus indeed. You are correct. Many people prefer not to think. What matters is that the time between exchanges is larger than the relaxation, which hence is system dependent, and that you have sufficient number of exchanges to equilibrate the T-dependent properties (which can be challenging). Our old paper is one of the few where this succeeded for a peptide because it is so small :). Marvin Seibert, Alexandra Patriksson, Berk Hess and David van der Spoel: Reproducible polypeptide folding and structure prediction using molecular dynamics simulations J. Mol. Biol. 354 pp. 173-183 (2005) David van der Spoel and M. Marvin Seibert: Protein Folding Kinetics and Thermodynamics from Atomistic Simulations Phys. Rev. Lett. 96 pp. 238102 (2006) This optimum ratio is, as far as I understand, derived assuming that the exchange attempt frequency is constant and that the protein dynamics are not limiting the diffusion of a replica up and down the temperature ladder. In a real system there will be some time-scale associated with the relaxation of the protein as it moves from one temperature to another. The rate of diffusion of the replica on the temperature ladder could potentially be limited by these protein dynamics or by the exchange frequency. If we are limited by the exchange frequency, then it would make sense to decrease the interval between exchange attempts to the same time-scale as the potential energy correlation time, and to choose the number of replicas such that the acceptance ratio was around 0.2. If we are limited by the protein dynamics then the exchange frequency doesn't matter, so the acceptance ratio should have no effect (as long, of course, as it isn't so low that the exchange frequency becomes limiting). This would mean for simulations of large proteins where the protein dynamics are limiting, we can slash the number of replicas required for an efficient REMD simulation. However, I haven't seen any simulations in the literature using very small acceptance ratios, which makes me suspicious of my logic. Does anyone have any thoughts on this? Cheers, Ben -- 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.sehttp://folding.bmc.uu.se -- 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] Graphene - force field
Hello, I am trying to run simulation of graphene oxide. I have 16 carbon atoms of same type. I am using opls force field. could make the .itp file and pasted here [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_071 CG 6 12.01100 0.00 A 3.5e-01 2.92880e-01 opls_072 CO 6 12.01100 0.265 A 3.5e-01 3.59824e-01 opls_116 OH 8 15.99940 -0.683 A 3.12000e-01 7.11280e-01 opls_117 HO 1 1.00800 0.418 A 0.0 0.0 [ bondtypes ] ; ij func b0 kb COOH 10.14100 133888.0 OHHO 10.09600 231375.0 CGCG 10.14000 392459.2 ; TRP,TYR,PHE CGCO 10.14000 392459.2 ; TRP,TYR,PHE [ angletypes ] ; ijk func th0 cth CG CO OH 190.000292.880 CO OH HO 1 108.500230.120 CG CG CG 1 120.000527.184 ; TYR(OL) [ dihedraltypes ] ; ijkl func coefficients ; OPLS Fourier function (func=5) CJ CJ CJ CJ 3 30.33400 0.0 -30.33400 0.0 0.0 0.0 ; CG CO OH HO 3 0.0 0.0 6.27600 0.0 CG CG CO OH 3 7.15882 -2.09200 2.77399 0.0 My question how can I step for the parameters ffoplsaa.rtp file. I made the parameters as follow [ SMA ] [ atoms ] CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CO opls_072 0.265 2 CG opls_071 0.00 1 CG opls_071 0.00 1 CO opls_072 0.265 2 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 OH opls_116-0.683 3 HO opls_117 0.000 4 OH opls_116-0.683 3 HO opls_117 0.000 4 [ bonds ] CG CG CG CO CO OH OH HO I am geting trouble to create .top file using pdb2gmx. Can you tell how to set up force field parameter for graphene. I am usinng Gromacs VERSION 4.0.7. Thanks Nilesh -- 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 Coulomb SR and Coulomb 14?
Dear experts, Can you please make me understand the actual difference between Coulomb SR and Coulomb 14? -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- 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 Coulomb SR and Coulomb 14?
On 13/01/2012 4:41 PM, Saba Ferdous wrote: Dear experts, Can you please make me understand the actual difference between Coulomb SR and Coulomb 14? See manual 3.4.7 for short-range interactions and 4.6.1 for 1-4. 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
Re: [gmx-users] Graphene - force field
On 13/01/2012 2:22 PM, Nilesh Dhumal wrote: Hello, I am trying to run simulation of graphene oxide. I have 16 carbon atoms of same type. I am using opls force field. could make the .itp file and pasted here [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 You need to choose some actual values here, not comment them out. ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_071 CG 6 12.01100 0.00 A 3.5e-01 2.92880e-01 opls_072 CO 6 12.01100 0.265 A 3.5e-01 3.59824e-01 opls_116 OH 8 15.99940 -0.683 A 3.12000e-01 7.11280e-01 opls_117 HO 1 1.00800 0.418 A 0.0 0.0 [ bondtypes ] ; ij func b0 kb COOH 10.14100 133888.0 OHHO 10.09600 231375.0 CGCG 10.14000 392459.2 ; TRP,TYR,PHE CGCO 10.14000 392459.2 ; TRP,TYR,PHE [ angletypes ] ; ijk func th0 cth CG CO OH 190.000292.880 CO OH HO 1 108.500230.120 CG CG CG 1 120.000527.184 ; TYR(OL) [ dihedraltypes ] ; ijkl func coefficients ; OPLS Fourier function (func=5) CJ CJ CJ CJ 3 30.33400 0.0 -30.33400 0.0 0.0 0.0 ; CG CO OH HO 3 0.0 0.0 6.27600 0.0 CG CG CO OH 3 7.15882 -2.09200 2.77399 0.0 My question how can I step for the parameters ffoplsaa.rtp file. I made the parameters as follow [ SMA ] [ atoms ] CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CO opls_072 0.265 2 CG opls_071 0.00 1 CG opls_071 0.00 1 CO opls_072 0.265 2 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 CG opls_071 0.00 1 OH opls_116-0.683 3 HO opls_117 0.000 4 OH opls_116-0.683 3 HO opls_117 0.000 4 [ bonds ] CG CG CG CO CO OH OH HO You should look at some example .rtp entries. You need to give a unique name to each atom, and to describe which are bound to which. Chapter 5 is your friend, read its examples. Mark I am geting trouble to create .top file using pdb2gmx. Can you tell how to set up force field parameter for graphene. I am usinng Gromacs VERSION 4.0.7. Thanks Nilesh -- 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
