[gmx-users] Simulation crashing

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Aug 29 10:17:25 CEST 2005

Hi Bob,

Just try 
trjconv -f initial.g96 -s initial.g96 -o initial.pdb -pbc inbox
and have a look at the structure with rasmol, pymol or any other *mol;
you'll see that you have severe overlaps, which will cause the system
to explode. You can't do something like this just by pasting in some
extra molecules!

What you should do is extend your box to create a vacuum layer, and
fill that with methanol. Don't forget to first do energy minimization.

Hope it helps,


On 8/27/05, Bob Johnson <robertjo at physics.upenn.edu> wrote:
> 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
> nanotube.
> 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?
> Thanks,
> Bob Johnson
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciencesand Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

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