Hello dear gmx-users! So, I run md and got all files md.cpt, .trr, .gro, mdf.xvg,... etc. then I did: grompp_d -f sp.mdp -c md.gro -n index.ndx -p topol.top -o sp.tpr where sp.mdp differ from md.mdp in one line: energygrps = Protein SOL (in md.mdp: energygrps = System) after that I did: mdrun_d -s sp.tpr -pf spf -rerun md.trr and got file spf.xvg, but there was no forces:
@ title "Pull force" @ xaxis label "Time (ps)" @ yaxis label "Force (kJ/mol/nm)" @TYPE xy 0.000000 0.000000 20.000000 0.000000 40.000000 0.000000 60.000000 0.000000 80.000000 0.000000 100.000000 0.000000 120.000000 0.000000 140.000000 0.000000 160.000000 0.000000 180.000000 0.000000 200.000000 0.000000 Also while reading frame I had a warning: WARNING: Some frames do not contain velocities. Ekin, temperature and pressure are incorrect, the virial will be incorrect when constraints are present. But I have no idea how to fix this. Help me, please. Sincerely. Petr. 11 октября 2010 г. 6:33 пользователь Dallas Warren <dallas.war...@monash.edu > написал: > The error has told you, you have repeat energy groups, where at least one > (and in your case all) of the atoms are placed within two energy groups. > > > > Solution, define your energy groups so that you don't have atoms in more > than one. > > > > You currently have: > > energygrps = Protein Protein > > > > Should be something like > > energygrps = Protein SOL > > > > Catch ya, > > Dr. Dallas Warren > > Medicinal Chemistry and Drug Action > > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > dallas.war...@monash.edu > > +61 3 9903 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > > *From:* gmx-users-boun...@gromacs.org [mailto: > gmx-users-boun...@gromacs.org] *On Behalf Of *???? ????? > *Sent:* Monday, 11 October 2010 4:13 AM > *To:* jalem...@vt.edu; Discussion list for GROMACS users > *Subject:* Re: [gmx-users] output force > > > > Unfortunately I've got an error. > > This is .mdp file: > > title = title > cpp = /lib/cpp > integrator = md > tinit = 0.0 > dt = 0.002 > nsteps = 25000 > nstcomm = 1 > comm_grps = System > ld_seed = -1 > niter = 40 > nstxout = 10000 > nstvout = 0 > nstfout = 0 > nstlog = 500 > nstenergy = 100 > nstlist = 10 > ns_type = grid > rlist = 1.2 > coulombtype = PME > rcoulomb = 1.2 > fourierspacing = 0.12 > pme_order = 4 > optimize_fft = yes > pbc = xyz > vdwtype = Cut-off > rvdw = 1.2 > tcoupl = V-rescale > tc_grps = System > tau_t = 0.1 > ref_t = 300.0 > annealing = single > annealing_npoints = 3 > annealing_time = 0 5 50 > annealing_temp = 5 300 300 > pcoupl = berendsen > pcoupltype = isotropic > compressibility = 4.5e-5 > tau_p = 10.0 > ref_p = 1.0 > gen_vel = yes > gen_temp = 5.0 > gen_seed = -1 > constraints = all-bonds > constraint_algorithm = Lincs > lincs_order = 4 > disre = simple > disre_weighting = conservative > disre_mixed = no > nstdisreout = 50000 > disre_tau = 0 > pull = constraint > pull_geometry = distance > pull_dim = Y Y Y > pull_constr_tol = 1e-6 > pull_nstfout = 1 > pull_nstxout = 1 > pull_ngroups = 1 > pull_group0 = a > pull_group1 = b > pull_init1 = 0.700 > pull_start = no > pull_k1 = 1000 > lincs_iter = 2 > energygrps = Protein Protein > > I just replace in .mdp file line energygrps = System and the error is: > > Fatal error: > Atom 1 in multiple Energy Mon. groups (1 and 2) > > What should I do to avoid this? > > > 10 октября 2010 г. 20:01 пользователь Петр Попов <magistrpet...@gmail.com> > написал: > > Thank you very much! > > 10 октября 2010 г. 19:58 пользователь Justin A. Lemkul <jalem...@vt.edu> > написал: > > > > > > Петр Попов wrote: > > So if I want to get protein-solvent component I should add in .mdp: > > energygrps = Protein SOL > > ? > > > > Yes, and set nstlist = 1. > > -Justin > > 10 октября 2010 г. 16:41 пользователь Justin A. Lemkul > <jalem...@vt.edu<mailto: > jalem...@vt.edu>> написал: > > > > > > Петр Попов wrote: > > Thank you for response! > One more question: > How can I get file with energy groups? Should I use grompp with > a -e ener.edr option? In this case, how to build ener.edr file? > > > The "energrygrps" keyword is an .mdp option, so generate a new .tpr > file with the desired groups and use the -rerun feature of mdrun on > the trajectory that has already been produced. > > -Justin > > 9 октября 2010 г. 14:50 пользователь Mark Abraham > <mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au> > <mailto:mark.abra...@anu.edu.au > <mailto:mark.abra...@anu.edu.au>>> написал: > > > You can get that with cunning use of energy groups and mdrun > -rerun, > but not mid-simulation. > Mark > > ----- Original Message ----- > From: Петр Попов <magistrpet...@gmail.com > <mailto:magistrpet...@gmail.com> > > <mailto:magistrpet...@gmail.com > <mailto:magistrpet...@gmail.com>>> > Date: Saturday, October 9, 2010 21:41 > Subject: [gmx-users] output force > To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> > > <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> > > > Hello dear gmx-users! > > > > When calculated forces in gromacs to produce pmf, we have > the net > force in output. For example: > > ... > > # > > # Giving Russians Opium May Alter Current Situation > > # > > @ title "Pull force" > > @ xaxis label "Time (ps)" > > @ yaxis label "Force (kJ/mol/nm)" > > @TYPE xy > > 0.000000 1017490.761270 > > 0.002000 -253098.034916 > > 0.004000 -43856.400160 > > 0.006000 48980.619113 > > 0.008000 52103.053067 > > 0.010000 33788.090031 > > 0.012000 19096.388350 > > 0.014000 14094.738810 > > 0.016000 14027.621966 > > 0.018000 15162.993741 > > 0.020000 14136.978177 > > ... etc. > > > > What sould I do to get the net force of protein-solvent > interactions or protein-protein interactions or solvent-solvent > interactions instead and get output .xvg file in the form > like this: > > > > time Force(type1) Force(type2) Force(type3) > > > > t1 f1 f1 f1 > > t2 f2 f2 f2 > > t3 f3 f3 f3 > > ... ... ... ... > > etc. > > > > Thank you for attention and I hope you will help me! > > -- > > gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > > <mailto:gmx-users@gromacs.org <mailto: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 > <mailto:gmx-users-requ...@gromacs.org> > <mailto:gmx-users-requ...@gromacs.org > <mailto:gmx-users-requ...@gromacs.org>>. > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > > <mailto:gmx-users@gromacs.org <mailto: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 > <mailto:gmx-users-requ...@gromacs.org> > <mailto:gmx-users-requ...@gromacs.org > > <mailto:gmx-users-requ...@gromacs.org>>. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- gmx-users mailing list gmx-users@gromacs.org > <mailto: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 > <mailto:gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > 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 >
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