[gmx-users] Error after trjconf processing

Mark Abraham mark.j.abraham at gmail.com
Fri May 3 15:26:05 CEST 2013

On Fri, May 3, 2013 at 3:17 PM, James Starlight <jmsstarlight at gmail.com>wrote:

> Mark,
> but if I run npt equilibration onto minimized structure (without
> velocities)  without definition of the new velocities in the npt.mdp file
> gen_vel = No
> I noticed that in npt.gro file velocities present. Have it been assigned
> inspite on
> gen_vel = No in mdp?

I can't answer - I don't know from your description and filename what was in
1) the coordinte file you input to the EM grompp,
2) the .gro file you got out of EM mdrun (which presumably went into the
NPT grompp),
3) the .tpr file you got out of NPT grompp, and
4) the .gro file you got out of NPT mdrun (which will always have
velocities regardless of the foregoing)

Please respect your reader's time and describe your observations carefully

I think there should never be velocities in 2. Velocities in 3 should
follow what the .mdp file said (but if 2 wrote velocities, then it is
conceivable that those are still the velocities in 3 iff gen_vel=no, but
you would have to inspect the values with gmxdump to see what was


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