[gmx-users] lincs warning

[XAvier Periole]

On Jun 3, 2009, at 10:58 AM, Giovanni Bussi wrote:

> Dear Xavier,
>
> With the default flag for pbc (periodic_molecules=no) you may end up
> in lincs problem if an atom of the protein becomes too close to the
> image of another atom of the protein.
>
> If this is your case, use periodic_molecules=yes, or enlarge the  
> solvation cell.
Thanks, I have however a very large water box and no problem there I  
believe.
>
> Hope this helps,
>
> Giovanni
>
>
>
> On Wed, Jun 3, 2009 at 10:48 AM, Erik Marklund  
> <erikm at xray.bmc.uu.se> wrote:
>> XAvier Periole skrev:
>>>
>>> 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 ?
>>>
>> If you use dynamic load balancing then you are sacrificing binary
>> reproducibility. Because of this, and the chaotic nature of MD, the  
>> error
>> will likely not occur at the same point in your continuation.  
>> Still, the
>> source of the error persists and is what demands attention I'd say.
>>>
>>> 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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>>
>> --
>> -----------------------------------------------
>> Erik Marklund, PhD student
>> Laboratory of Molecular Biophysics,
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,    75124 Uppsala, Sweden
>> phone:    +46 18 471 4537        fax: +46 18 511 755
>> erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys
>>
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