[gmx-users] output force - 2

[Justin A. Lemkul]

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 <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.
> 
>     -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

========================================