[gmx-users] MDrun rerun issue

Mark Abraham mark.j.abraham at gmail.com
Tue Jan 30 11:10:27 CET 2018


Good initiative, but unfortunately mdrun -rerun is unfit for pretty much
anything connected with the velocities. See
https://redmine.gromacs.org/issues/1868 for the gory details.

The potential energy should be fine (unless you are introducing a
periodicity artifact in how you are using trjconv), but why are you
involving trjconv at all? gmx mdrun -rerun prdv.trr works.


On Tue, Jan 30, 2018 at 10:37 AM dodia <dodia at mpip-mainz.mpg.de> wrote:

> Dear gromacs users,
> I am new user and trying to learn about the software by running simple
> water box simulations. I did a 15ns NVT simulation of around 80 water
> molecules (after 1.5ns+1.5ns of NVT & NPT equilibration) at 300K and the
> resultant data seemed reasonably accurate wrt density and average
> temperature. Now I tried to extract 50 frames from the trajectory and
> stored them in a .gro file (with positions+velocities) and tried to use
> mdrun -rerun to crosscheck energies, but in the resultant log file, the
> temperature varies around 7000K, potential energy becomes positive and
> other values go haywire. Can anyone help me with this issue? I used the
> following commands after production calculation:
> echo 1 | gmx trjconv -f prdv.trr -s prdv.tpr -vel -dt 100 -box 1.32 1.32
> 3.5 -o frame.gro
> gmx mdrun -s prdv.tpr -rerun frame.gro -g test.log
> prdv is the file suffix for production simulation. prdv.trr contains all
> the positions, velocities and forces at every 1.5ps
> Best Regards,
> Mayank Dodia
> --
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