[gmx-users] simulation crash

[Anton Feenstra]

herbst at fhi-berlin.mpg.de wrote:
> I use constraints on the c-alpha atoms, so the helix should be stable.
> I of course optimized the starting geometry, I tried to use the output
> geometry of a 600 K run as input file, and I tried the simulation with a
> larger box, but none of this worked. What else can I try ? What could be
> going wrong ?

Constraints can make your simulation unstable, especially if there are 
many and/or they are very tight. The problem is that tight (or many) 
constraints are prone to high-frequency oscillations, which may be too 
fast for the integration timestep that you are using. (But, that does 
not explain why your 600K simulations do not crash...)

Have you tried slowly (e.g. over several 100 ps) decreasing the 
temperature, e.g. using the simulated annealing option?


-- 
Groetjes,

Anton

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