[gmx-users] Maximal nrexcl

[Mark Abraham]

Or use rerun with each pair of molecules alone, by constructing a large
number of sets of matching input subsets from using tpbconv and trjconv.

Mark

On Jan 21, 2014 4:54 AM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>
> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
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