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 <[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
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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