Is the way to decompose pull force? 2010/10/12 Justin A. Lemkul <[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 | (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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