[gmx-users] Removing velocities from restart file

[Bob Johnson]

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?
Thanks,
Bob Johnson