[gmx-users] output force - 2
magistrpetrus at gmail.com
Tue Oct 12 16:04:12 CEST 2010
Is it possible to slightly change the source code to adjust output of
pullf in appropriate form? And if it is, how?
12 октября 2010 г. 17:49 пользователь Justin A. Lemkul
<jalemkul at 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.
>> 2010/10/12 Justin A. Lemkul <jalemkul at vt.edu <mailto: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 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.
>> 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 <http://vt.edu> | (540) 231-9080
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> 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
> gmx-users mailing list gmx-users at gromacs.org
> 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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