[AMBER] sander and pmemd

From: xiaojiong <xiaojiong.zju.edu.cn>
Date: Thu, 26 Apr 2012 19:56:18 +0800

Dear sir/madam,

I am a user of AMBER in China. My system is a protein complex with 214 AA residues. Now I am doing the production phase with sander before MMPBSA calculation. But it seems rather slow.

I noticed that pmemd is an optimized version of sander for speed and for parallel scaling. And I have two questions here.

Q1: As I modeled my system in the first 1ns with sander, whether it is proper to turn to use pmemd in the last several ns for the purpose of speed?
Q2: Will the results from sander and pmemd be the same? What is the difference between the two algorithms?

Thanks for your time!

Cao Yang,
Zhejiang University, China
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Received on Thu Apr 26 2012 - 05:00:03 PDT
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