[gmx-users] Maximal nrexcl

Justin Lemkul jalemkul at vt.edu
Tue Jan 21 04:40:29 CET 2014



On 1/20/14, 8:17 PM, cynthiahong1983 wrote:
> Dear All,
>
> Does anyone know whether there is a maximal limit for nrexcl?
>
> I tried to calculate the intermolecular energy between polymeric molecules through "mdrun -rerun" and a large "nrexcl". But when the molecule becomes very long e.g. having ~ 20 bonds in the backbone and I set nrexcl = 20 , grompp beccame very slowly and just terminated in error like "4210 terminated" (the number changed each time when it failed.)
>
> Someone ever met with similar situations?
>

The only real limitation is available memory.  For this case, you'd need a lot 
of it.  The other option (depending on how many polymers you have) would be to 
assign each one to individual energygrps in the .mdp and .ndx files.

-Justin

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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