[gmx-users] output force - 2

Петр Попов magistrpetrus at gmail.com
Tue Oct 12 08:25:18 CEST 2010

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.

Help me, please.

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