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looking for implicit solvent (parallel, images)
#21788 08/20/09 12:29 PM
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Hello,

I'm looking for an implicit solvent implementation that allows me to run it in parallel and allows to have images. It seems as if GBMV doesn't support images while GBSW doesn't seem to run in parallel (at least the performance doesn't change a lot when I add processors). Could somebody please give me some advice on which module I should try? Thanks,

Alexander

Re: looking for implicit solvent (parallel, images)
Melbourne #21789 08/20/09 12:56 PM
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PBC and implict solvent are rarely used together. For confinement there are other options (than PBC) available in CHARMM (cons.doc and mmfp.doc). GBSW is parallel, but I do not know how well this works.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: looking for implicit solvent (parallel, images)
lennart #21790 08/20/09 01:10 PM
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Thanks for the quick answer. In my case PBCs would be better than an artificial confinement...but it seems as if I'll have to live with that. And it seems as if GBSW is in fact parallel...but going from 8 to 16 processors doesn't give any speedup (genborn accounts for ~97% of the CPU time).

Alexander


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