[gmx-users] lincs warning

Ran Friedman r.friedman at bioc.uzh.ch
Wed Jun 3 10:01:29 CEST 2009

Hi XAvier,
Do you use virtual sites? I've seen this when I used virtual sites,
large time steps and a system that probably wasn't equilibrated enough.

XAvier Periole wrote:
> Dears,
> I am experiencing some problems running a few proteins in water
> (GROMOS43a1/SPC)
> with gmx-4.0.4 using 32 CPUs.
> After some ns lincs warnings appear and eventually the simulation
> crashes dues
> to too many lincs warnings.
> When restarting the simulation feeding "-cpi md.cpt" to mdrun the
> simulation restarts
> fine and no lincs warning are reported on the same portion of the
> simulation. The
> simulation runs again for some ns and the same happens: new lincs
> warning appear
> and eventually the simulation crashes again.
> Any explanation for this? Any solution?
> Best,
> XAvier.
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