Is it possible to slightly change the source code to adjust output of pullf in appropriate form? And if it is, how?
Petr. 12 октября 2010 г. 17:49 пользователь Justin A. Lemkul <jalem...@vt.edu> написал: > > > Петр Попов wrote: >> >> Is the way to decompose pull force? >> > > None that I'm aware of. The only terms that (I think) can be decomposed are > short-range nonbonded interactions, using energygrps. > > You might be able to extract forces on subsets of atoms using g_traj, if > you've saved forces at suitable intervals (nstfout) in the .trr file. > > -Justin > >> 2010/10/12 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>> >> >> >> >> Петр Попов wrote: >> >> 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. >> >> >> I'll take a guess, but that's all it will be. When using mdrun >> -rerun with new energygrps, the only difference is the terms that >> are written to the .edr file. You will not get a different >> pullf.xvg file. The pull force between two groups is independent of >> the groups you've set for simple output control, anyway. That's all >> that energygrps will do for you - decompose nonbonded terms between >> the selected groups. >> >> Probably the pull code is dependent upon some of the missing terms. >> From the warning you get, I suspect that you didn't save velocities >> in the .trr file, so some energy terms will be incorrect, as you're >> being told. I doubt, however, that even if you had velocities, the >> pullf.xvg file would change. >> >> -Justin >> >> >> Help me, please. >> >> Sincerely. >> Petr. >> >> >> -- ======================================== >> >> 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-us...@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-us...@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
