[gmx-users] lincs warning
x.periole at rug.nl
Wed Jun 3 10:07:31 CEST 2009
On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote:
> Hi XAvier,
> Do you use virtual sites? I've seen this when I used virtual sites,
No virtual sites.
> large time steps and a system that probably wasn't equilibrated
time step 2 fs and a system totally equilibrated, nothing there.
I would have considered this if the warning were reproduced when
restarting the simulation.
It seems more that it is a loss of accuracy due to communication
between CPUs ?
> XAvier Periole wrote:
>> I am experiencing some problems running a few proteins in water
>> 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?
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