[gmx-users] Error after trjconf processing
jmsstarlight at gmail.com
Fri May 3 20:30:06 CEST 2013
The problem was solved by adding -pbc mol -ur compact flags to the trjconv.
So the problems were indeed in pbc conditions
2013/5/3 Mark Abraham <mark.j.abraham at gmail.com>
> On Fri, May 3, 2013 at 3:17 PM, James Starlight <jmsstarlight at gmail.com
> > 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
> 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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