Re: [AMBER] MMPBSA.py decomposition option

From: Hannes Kopitz <hannes.kopitz.gmx.de>
Date: Wed, 11 Jul 2012 05:45:05 +0200

Dear Komath,

The per-residue decomp shouldn't actually be significantly slower than doing the same calculations w/o decomp since here the PB equation is solved once per structure. But of course it's slow compaired to GB.
But for the pairwise decomp the PB equation needs to be solved once per any residue (taken into account) per structure. Accordingly it should be limited to some residues of interest.

Cheers!
Hannes

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"Damodaran, Komath" <Komath.Damodaran.elan.com> schrieb:
Hi,
The decomposition option 4 (i.e, pair-wise decomposition with 1-4 contributions added to the respective nonbond terms) with PB solvent, is inordinately slow, vis-à-vis the residue-wise decomposition. Is there any documentation on how exactly these decompositions are done and explaining this behavior?
Thanks very much!
Dam
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Received on Tue Jul 10 2012 - 21:00:03 PDT