[AMBER] GBSA speeds for big molecules

From: Asmit Bhowmick <asmit.berkeley.edu>
Date: Tue, 27 Jan 2015 13:18:16 -0800

Hello Amber users,

I am trying to do an MD simulation of a big protein(~ 22,000 atoms) with
Amber12 software. The 1st thing I tried was to use GBSA with Amberff99SB
given the system size. However, the speeds I am getting are surprisingly
slow. On 64 cores of an AMD opteron 6274 processor(2.2 Ghz) using PMEMD and
using 16 A cutoffs for both VdW and rgbmax, I get about 0.2 ns/day (~ 300
ms/step). Are these the standard speeds to expect on such a big system with
GBSA ? Are there any suggested methods to simulate such a big protein ?

Asmit Bhowmick
Department of Chemical Engineering
University of California at Berkeley
Teresa Head-Gordon group
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Received on Tue Jan 27 2015 - 13:30:03 PST
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