[gmx-users] lincs warning

[XAvier Periole]

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  
> enough.
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.

> Ran.
>
> 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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>
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