----- Original Message ----- From: "Justin A. Lemkul" <[email protected]> Date: Wednesday, October 13, 2010 0:50 Subject: Re: [gmx-users] output force - 2 To: Gromacs Users' List <[email protected]>
> > > 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. Maybe, but they won't be forces decomposed group-wise. I've not a clue how the pull force relates to the forces on the atoms, but you can probably get group-wise forces by using mdrun -rerun with well-chosen energy groups, energy group exclusions, and nstfout=1. You will likely need several iterates if you want several decomposed terms. Mark > >2010/10/12 Justin A. Lemkul <[email protected] > <mailto:[email protected]>>> > > > > > > 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 [email protected] > > <mailto:[email protected]> > > > 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- > [email protected]> <mailto:gmx-users- > [email protected]>.> 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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