[gmx-users] Crush after ~135 ps

David spoel at xray.bmc.uu.se
Thu Jul 10 08:50:01 CEST 2003

On Thu, 2003-07-10 at 08:07, Semen Esilevsky wrote:
> Dear GMX users,
> Thanks to your help I've set up a simulation of my
> protein. It was expected to be 1ns run, however it
> crashed after ~135 ps.
> The last message in the log was something like this:
> "Can't set a water molecule starting from atom ###,
> fatal error at bla-bla-bla.c line ###", than I was
> asked to reduce the step size or to check the system. 

one possibility is that a water molecule is trapped in a hydrophobic
environment without hydrogen bonds. Then it may start spinning and the
Settle error can occur. This is usually quite hard to find out because
you need to know the velocity of the molecule. If you know which water
it is (written in the log file) you can try to animate the trajectory.

Assigning new velocities and/or continuing the trajectory from, say, 100
ps might be enough to get over this problem.

> The system was solwated by ~8000 water molecules in a
> rectangular box. PME with the defauls params from the
> manual was used.
> So far I've found several suspicious points:
> 1) Too short equilibration of the solvent with
> restrained protein
> 2) Exposure of the hydrophobic areas in the protein
> (it  is a membrane protein, but I put it into the box
> of water)
> 3) The system is not neutral (+7)
> However, I still can't understand why the simulation
> crashed after quite long successful run. 
> Any ideas how to fix this problem?
> Sincerely,
> Semen
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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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