[gmx-users] Removing velocities from restart file

David van der Spoel spoel at xray.bmc.uu.se
Sat Aug 27 20:59:38 CEST 2005

On Sat, 2005-08-27 at 14:31 -0400, Bob Johnson wrote:
> Hello again,
> I have a restart file (restart.g96) for my nanotube, DNA, and water. Again, the
> DNA is halfway in the next periodic box. I can successfully restart a
> simulation using this file as the initial configuration and GROMACS recognizes
> that the truncated DNA pieces are actually bonded together.
> However, when I remove the velocity portion of the restart file, GROMACS no
> longer recognizes that the DNA pieces are bonded together. Eventually the
> program crashes. In fact, something very dramatic takes place in the
> trajectory. About 3 frames before the program crashes, the DNA disappears and
> the nanotube atoms all start flying to one point in space. Everything
> eventually disappears from the trajectory and then the program crashes. Why
> does removing the velocity portion of the restart file mess everything up?
compare tpr files with and without vel. using gmxcheck.

> Thanks,
> Bob Johnson
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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