[gmx-users] output force - 2

[Justin A. Lemkul]

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

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