[gmx-users] output force - 2
magistrpetrus at gmail.com
Tue Oct 12 14:33:53 CEST 2010
Is the way to decompose pull force?
2010/10/12 Justin A. Lemkul <jalemkul at 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
>> 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
> Help me, please.
> 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
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