Re: [gmx-users] RE: Targeted MD
Hi, -r and -rb are for FEP. If you want to bias your simulation's sampling, you can use the pull code, essential dynamics sampling or flooding, all of which are described in the manual and literature. Ran Nimesh Jain wrote: > Hello, > > I realize that this topic has been discussed before, but I just need > to ascertain a few things: I have a system of about 1400 atoms with > implicit solvent and I want to do a targeted MD. While doing the > pre-processing, if I just specify "grompp -r in.gro -rb out.gro", is > this sufficient or are there any other things that I need to consider. > Also, I have tabulated potentials. > > If any one knows how to do this, or if you need more info on my > system, please let me know. > > Thanks, > Nimesh -- 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] RE: Targeted MD
Hello, I realize that this topic has been discussed before, but I just need to ascertain a few things: I have a system of about 1400 atoms with implicit solvent and I want to do a targeted MD. While doing the pre-processing, if I just specify "grompp -r in.gro -rb out.gro", is this sufficient or are there any other things that I need to consider. Also, I have tabulated potentials. If any one knows how to do this, or if you need more info on my system, please let me know. Thanks, Nimesh -- 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] Re: Targeted MD
Steven Kirk wrote: Mark Abraham <[EMAIL PROTECTED]> wrote "Non-Protein" serves well here. So a usual tc-grps line has "Protein Non-Protein" for a protein simulation. Mark A supplementary question. The tc-grps line can take predefined standard group names such as 'System', 'Protein' and 'Non-Protein'. Does the 'Protein' group need to actually BE a protein, or are 'Protein' and 'Non-Protein' really synonyms for 'PresumablyBigMoleculeOfInterestProteinOrNot' and 'EverythingElse' ? I haven't read the code or found any mention in the manual, but I expect that src/share/top/aminoacids.dat contains the names of any amino acids, and thus implicitly defines these groups. Mark ___ 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: [Bulk] Re: [gmx-users] Re: Targeted MD
Protein are defined by the residue names inside aminoacids.dat. So, it is possible for nucleic acid to be "Protein". Steven Kirk wrote: Mark Abraham <[EMAIL PROTECTED]> wrote Subject: Re: [gmx-users] Re: Targeted MD To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed wei-xin xu wrote: > Some hints on practices that generally *not a good idea* to use: > > * Do not use separate thermostats for different components of your > system. Some molecular dynamics thermostats only work well in the > thermodynamic limit. If you use one thermostat for, say, a small > molecule, another for protein, and another for water, you are > likely introducing errors and artifacts that are hard to predict. > In particular, do not couple ions in aqueous solvent differently > from that > * solvent. > > Sorry that I do not actually understand here. The link I copied above > shows that better not to "couple ions in aqueous solvent differently > from that solvent". Maybe not separately but differently (mean different > temperature)? "differently" is intended to mean "in a separate group". I'll reword my wiki sentence. The original poster showed an .mdp file where tc-grps = Protein ; SOL CL UNK (or something like that). Now actually, the semicolon starts a comment, so he's only thermostatting the protein. That's a bad idea because it will lead to net heat flow from the protein to the rest of the system. Even if there were no semicolon, there are probably a few thousand solvent molecules and a handful of chloride ions. Temperature is defined from the average kinetic energy, and the average kinetic energy of a handful of ions in thermal contact with many other atoms will have large fluctuations, and this will lead to the thermostat doing lots of corrections, for lots of heat flow in and out of the system. So treating solvent+ions+other_small_stuff as one group for T-coupling purposes is a good idea, and the standard group "Non-Protein" serves well here. So a usual tc-grps line has "Protein Non-Protein" for a protein simulation. Mark A supplementary question. The tc-grps line can take predefined standard group names such as 'System', 'Protein' and 'Non-Protein'. Does the 'Protein' group need to actually BE a protein, or are 'Protein' and 'Non-Protein' really synonyms for 'PresumablyBigMoleculeOfInterestProteinOrNot' and 'EverythingElse' ? Thanks! Steve Kirk ___ 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] Re: Targeted MD
Mark Abraham <[EMAIL PROTECTED]> wrote Subject: Re: [gmx-users] Re: Targeted MD To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed wei-xin xu wrote: > Some hints on practices that generally *not a good idea* to use: > > * Do not use separate thermostats for different components of your > system. Some molecular dynamics thermostats only work well in the > thermodynamic limit. If you use one thermostat for, say, a small > molecule, another for protein, and another for water, you are > likely introducing errors and artifacts that are hard to predict. > In particular, do not couple ions in aqueous solvent differently > from that > * solvent. > > Sorry that I do not actually understand here. The link I copied above > shows that better not to "couple ions in aqueous solvent differently > from that solvent". Maybe not separately but differently (mean different > temperature)? "differently" is intended to mean "in a separate group". I'll reword my wiki sentence. The original poster showed an .mdp file where tc-grps = Protein ; SOL CL UNK (or something like that). Now actually, the semicolon starts a comment, so he's only thermostatting the protein. That's a bad idea because it will lead to net heat flow from the protein to the rest of the system. Even if there were no semicolon, there are probably a few thousand solvent molecules and a handful of chloride ions. Temperature is defined from the average kinetic energy, and the average kinetic energy of a handful of ions in thermal contact with many other atoms will have large fluctuations, and this will lead to the thermostat doing lots of corrections, for lots of heat flow in and out of the system. So treating solvent+ions+other_small_stuff as one group for T-coupling purposes is a good idea, and the standard group "Non-Protein" serves well here. So a usual tc-grps line has "Protein Non-Protein" for a protein simulation. Mark A supplementary question. The tc-grps line can take predefined standard group names such as 'System', 'Protein' and 'Non-Protein'. Does the 'Protein' group need to actually BE a protein, or are 'Protein' and 'Non-Protein' really synonyms for 'PresumablyBigMoleculeOfInterestProteinOrNot' and 'EverythingElse' ? Thanks! Steve Kirk -- Dr. Steven R. Kirk <[EMAIL PROTECTED], [EMAIL PROTECTED]> Dept. of Technology, Mathematics & Computer Science (P)+46 520 223215 University West (F)+46 520 223299 P.O. Box 957 Trollhattan 461 29 SWEDEN http://beacon.webhop.org ___ 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] Re: Targeted MD
Thanks a lot for the detailed and nice explainations. 2008/1/10, Mark Abraham <[EMAIL PROTECTED]>: > > wei-xin xu wrote: > > > Some hints on practices that generally *not a good idea* to use: > > > > * Do not use separate thermostats for different components of your > > system. Some molecular dynamics thermostats only work well in the > > thermodynamic limit. If you use one thermostat for, say, a small > > molecule, another for protein, and another for water, you are > > likely introducing errors and artifacts that are hard to predict. > > In particular, do not couple ions in aqueous solvent differently > > from that > > * solvent. > > > > Sorry that I do not actually understand here. The link I copied above > > shows that better not to "couple ions in aqueous solvent differently > > from that solvent". Maybe not separately but differently (mean different > > temperature)? > > "differently" is intended to mean "in a separate group". I'll reword my > wiki sentence. > > The original poster showed an .mdp file where > > tc-grps = Protein ; SOL CL UNK > > (or something like that). Now actually, the semicolon starts a comment, > so he's only thermostatting the protein. That's a bad idea because it > will lead to net heat flow from the protein to the rest of the system. > Even if there were no semicolon, there are probably a few thousand > solvent molecules and a handful of chloride ions. Temperature is defined > from the average kinetic energy, and the average kinetic energy of a > handful of ions in thermal contact with many other atoms will have large > fluctuations, and this will lead to the thermostat doing lots of > corrections, for lots of heat flow in and out of the system. So treating > solvent+ions+other_small_stuff as one group for T-coupling purposes is a > good idea, and the standard group "Non-Protein" serves well here. So a > usual tc-grps line has "Protein Non-Protein" for a protein simulation. > > Mark > ___ > 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 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] Re: Targeted MD
wei-xin xu wrote: Some hints on practices that generally *not a good idea* to use: * Do not use separate thermostats for different components of your system. Some molecular dynamics thermostats only work well in the thermodynamic limit. If you use one thermostat for, say, a small molecule, another for protein, and another for water, you are likely introducing errors and artifacts that are hard to predict. In particular, do not couple ions in aqueous solvent differently from that * solvent. Sorry that I do not actually understand here. The link I copied above shows that better not to "couple ions in aqueous solvent differently from that solvent". Maybe not separately but differently (mean different temperature)? "differently" is intended to mean "in a separate group". I'll reword my wiki sentence. The original poster showed an .mdp file where tc-grps = Protein ; SOL CL UNK (or something like that). Now actually, the semicolon starts a comment, so he's only thermostatting the protein. That's a bad idea because it will lead to net heat flow from the protein to the rest of the system. Even if there were no semicolon, there are probably a few thousand solvent molecules and a handful of chloride ions. Temperature is defined from the average kinetic energy, and the average kinetic energy of a handful of ions in thermal contact with many other atoms will have large fluctuations, and this will lead to the thermostat doing lots of corrections, for lots of heat flow in and out of the system. So treating solvent+ions+other_small_stuff as one group for T-coupling purposes is a good idea, and the standard group "Non-Protein" serves well here. So a usual tc-grps line has "Protein Non-Protein" for a protein simulation. Mark ___ 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] Re: Targeted MD
wei-xin xu wrote: 2008/1/10, Mark Abraham <[EMAIL PROTECTED]>: Some hints on practices that generally not a good idea to use: Do not use separate thermostats for different components of your system. Some molecular dynamics thermostats only work well in the thermodynamic limit. If you use one thermostat for, say, a small molecule, another for protein, and another for water, you are likely introducing errors and artifacts that are hard to predict. In particular, do not couple ions in aqueous solvent differently from that solvent. Sorry that I do not actually understand here. The link I copied above shows that better not to "couple ions in aqueous solvent differently from that solvent". Maybe not separately but differently (mean different temperature)? I am actually a novice in Gromacs. It's a bit off-topic. The paragraph quoted above implies that "not separately" so it is generally applies to cases where you want to make a temperature-coupling group of a small number of particles ___ 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] Re: Targeted MD
2008/1/10, Mark Abraham <[EMAIL PROTECTED]>: > Stanislav Bobritsky wrote: > > > > Well, but (as I know from Manual, Ch. 6, p. 120) there is > > "approach to do targeted MD" in GMX. > > > > Did you add position restraint to your protein > > topology? > > > > > > No, I did not. > > What group must be restrained therefore? Whole protein or whole protein > > except loop? > > From "man grompp", > > > When using position restraints a file with restraint coordinates can be > > supplied with -r, otherwise restraining will be done with respect to the > > conformation from the -c option. For free energy calculation the the > > coordinates for the B topology can be supplied with -rb, otherwise they > will > > be equal to those of the A topology. > > Thus I expect your earlier grompp command line didn't do the job you > thought it did. > > You could restrain just the loop if you knew the protein was stable, but > easiest is to present conformation A as -c and B as -r. pdb2gmx will > have supplied you with a posre.itp file, and you need -DPOSRES in the > include .mdp directive so that the former works. > > Your .mdp file as supplied earlier should not T-couple only your solute, > and neither should it couple your counterions separately from the > solvent. See http://wiki.gromacs.org/index.php/Thermostats Some hints on practices that generally *not a good idea* to use: - Do not use separate thermostats for different components of your system. Some molecular dynamics thermostats only work well in the thermodynamic limit. If you use one thermostat for, say, a small molecule, another for protein, and another for water, you are likely introducing errors and artifacts that are hard to predict. In particular, do not couple ions in aqueous solvent differently from that - solvent. Sorry that I do not actually understand here. The link I copied above shows that better not to "couple ions in aqueous solvent differently from that solvent". Maybe not separately but differently (mean different temperature)? I am actually a novice in Gromacs. > Based on the foregoing, I'd guess that you're fairly new to MD and/or > GROMACS. I'd strongly recommend doing some (more) tutorials and > background reading so that you have more idea what "normal" MD is, and > the consequences of changes you might make. Otherwise the odds are > excellent you're just using an complicated quasi-random number generator. > > Mark > ___ > 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 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] Re: Targeted MD
Stanislav Bobritsky wrote: > Well, but (as I know from Manual, Ch. 6, p. 120) there is "approach to do targeted MD" in GMX. Did you add position restraint to your protein topology? No, I did not. What group must be restrained therefore? Whole protein or whole protein except loop? From "man grompp", When using position restraints a file with restraint coordinates can be supplied with -r, otherwise restraining will be done with respect to the conformation from the -c option. For free energy calculation the the coordinates for the B topology can be supplied with -rb, otherwise they will be equal to those of the A topology. Thus I expect your earlier grompp command line didn't do the job you thought it did. You could restrain just the loop if you knew the protein was stable, but easiest is to present conformation A as -c and B as -r. pdb2gmx will have supplied you with a posre.itp file, and you need -DPOSRES in the include .mdp directive so that the former works. Your .mdp file as supplied earlier should not T-couple only your solute, and neither should it couple your counterions separately from the solvent. See http://wiki.gromacs.org/index.php/Thermostats Based on the foregoing, I'd guess that you're fairly new to MD and/or GROMACS. I'd strongly recommend doing some (more) tutorials and background reading so that you have more idea what "normal" MD is, and the consequences of changes you might make. Otherwise the odds are excellent you're just using an complicated quasi-random number generator. Mark ___ 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] Re: Targeted MD
2008/1/9, Berk Hess <[EMAIL PROTECTED]>: > > > > > > > Date: Wed, 9 Jan 2008 15:30:38 +0200 > > From: [EMAIL PROTECTED] > > To: gmx-users@gromacs.org > > Subject: [gmx-users] Re: Targeted MD > > > > > > Ran Friedman wrote: > >>Dear Stanislav, > >> > >>AFAIK there's no "targeted MD" in GMX. You can run EDS or use the > >>flooding algorithm. > >> > >>Ran. > > > > Well, but (as I know from Manual, Ch. 6, p. 120) there is "approach to > do targeted MD" in GMX. > > Did you add position restraint to your protein > topology? No, I did not. What group must be restrained therefore? Whole protein or whole protein except loop? ___ 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] Re: Targeted MD
> Date: Wed, 9 Jan 2008 15:30:38 +0200 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] Re: Targeted MD > > > Ran Friedman wrote: >>Dear Stanislav, >> >>AFAIK there's no "targeted MD" in GMX. You can run EDS or use the >>flooding algorithm. >> >>Ran. > > Well, but (as I know from Manual, Ch. 6, p. 120) there is "approach to do > targeted MD" in GMX. Did you add position restraint to your protein topology? Berk. _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/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
Re: [gmx-users] Re: Targeted MD
Stanislav Bobritsky wrote: > *Ran Friedman wrote:* > >Dear Stanislav, > > > >AFAIK there's no "targeted MD" in GMX. You can run EDS or use the > >flooding algorithm. > > > >Ran. > > Well, but (as I know from Manual, Ch. 6, p. 120) there is "approach to do > targeted MD" in GMX. > Together with an explanation why one should not use it for proteins :-) But I guess you know what you need. When I read "targeted MD" I think about applying an external force in order to reduce the RMSD between two structures, so that the dynamics are somewhat perturbed, as it's done in CHARMM. Ran. ___ 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] Re: Targeted MD
*Ran Friedman wrote:* >Dear Stanislav, > >AFAIK there's no "targeted MD" in GMX. You can run EDS or use the >flooding algorithm. > >Ran. Well, but (as I know from Manual, Ch. 6, p. 120) there is "approach to do targeted MD" in GMX. S. Bobritsky, TSNU, Kiev Ukraine ___ 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] Re: Targeted MD
>Stanislav Bobritsky wrote: >>* Hello dear gromacs users! *>*> I`m trying to do targeted MD. I have two protein conformations which are *>*> different from each other by one loop position. I need to force *>*> conformation A to B. *>*> It was following commands executed: *>*> *>*> grompp -с box.gro -f md.mdp -r conf1.pdb -rb conf2.pdb -p topol.top -o *>*> transformer.tpr *>*> *>* > mdrun -s transformer.tpr -o -x -c -e -g -v *>*> *>*> But it can be viewed from traj.xtc that conformation didn`t change. *>*> Protein just spins (with speed increasing), and desired loop does not move. *>*> *>* > What can I do to fix it? *> >What's in your .mdp file? > >Mark .mdp file contains following: title= prot cpp = cpp define = -DFLEX_SPC integrator= md tinit= 0 dt = 0.001 nsteps = 100 init_step = 0 comm-mode= Linear nstcomm = 1 comm-grps= bd-fric = 0 ld-seed = 1993 emtol= 1000.0 emstep = 0.001 niter= 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr= 10 nstxout = 1000 nstvout = 2000 nstfout = 2000 nstcheckpoint= 1 nstlog = 100 nstenergy= 1000 nstxtcout= 1000 xtc-precision= 1000 xtc-grps = protein ;SOL UNK CL- energygrps = protein ;SOL UNK CL- nstlist = 10 ns_type = Grid pbc = xyz rlist= 0.9 domain-decomposition = no coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 epsilon_r= 1 epsilon_rf = 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.4 DispCorr = EnerPres table-extension = 1 energygrp_table = fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-5 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes gb_algorithm = Still nstgbradii = 1 rgbradii = 2 gb_saltconc = 0 implicit_solvent = No tcoupl = berendsen tc-grps = protein ; sol CL- UNK tau_t= 0.1 ; 0.1 0.1 0.1 ref_t= 298; 298 298 298 Pcoupl = no Pcoupltype = Isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 1.0 1.0 andersen_seed= 815131 gen-vel = no gen-temp = 298 gen-seed = 173529 constraints = all-bonds constraint-algorithm = Shake unconstrained-start = yes Shake-SOR= no shake-tol= 1e-04 lincs-order = 4 lincs-iter = 2 lincs-warnangle = 60 morse= no energygrp_excl = disre= No disre-weighting = Conservative disre-mixed = no disre-fc = 1000 disre-tau= 0 nstdisreout = 100 orire= no orire-fc = 0 orire-tau= 0 orire-fitgrp = nstorireout = 100 dihre= No dihre-fc = 1000 dihre-tau= 0 nstdihreout = 100 free-energy = no init-lambda = 0 delta-lambda = 0 sc-alpha = 0 sc-power = 0 sc-sigma = 0.3 Stanislav Bobritsky, ChemBio Center, Taras Shevchenko National University, Kiev, Ukraine. ___ 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
