[gmx-users] lincs warning

[Giovanni Bussi]

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.

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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>>>
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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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