[gmx-developers] bonded interaction -- single molecule in parallel gmx?
feenstra at chem.vu.nl
Tue Jul 29 16:50:28 CEST 2003
David van der Spoel wrote:
> On Tue, 2003-07-29 at 12:11, Fan Hao wrote:
>> I am trying to parallelize my implicit solvent model in gmx
>>but I met a problem from bonded interaction. I use LINCS for the
>>constraint in my sd simulation The system is only a protein molecule so
>>when I did "grompp -np 2 ..., gmx try to split the molecule between the
> how about using only constraints for the H atoms?
> there is no other simple solution.
Since LINCS is rather fast, couldn't you do it on all nodes that the
molecule is on? Or would they not give identical solutions then?
(Of course this will in the end kill your dcaling due to Amdahls law...)
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| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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