[gmx-users] Simulation crashing

Bob Johnson robertjo at physics.upenn.edu
Sat Aug 27 01:41:34 CEST 2005

Hello everyone,
This question may pertain to my previous post. My system consists of an infinite
nanotube, single stranded DNA and some water. I perform several simulations at
300K to equilibrate the system. In that time I observe the DNA binding to the

Now I want to add some methanol (just a small box of about 125 molecules) to the
system. I take the restart file (restart.g96) from the previous simulation that
only contained the nanotube, DNA, and water. I then concatenate the coordinates
of the methanol molecules at the end of the restart file and call it
initial.g96. I then start a new simulation using initial.g96 as my initial
configuration. MDRUN only generates 1 frame before it crashes. When I look at
the generated frame it's apparent that all the methanol atoms are exploding.

I have a separate topology file for the nanotube, DNA, water and methanol. When
I do a simulation of ONLY the methanol atoms, I get stable results. Thus it
seems that the methanol topology file and force field is fine. I've also tried
performing a simulation with the nanotube, DNA, water, and just one methanol
and it still crashes. Any suggestions?
Bob Johnson

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