Nmode on 10,000-atom probably takes long time, even if you do have plenty of
memory.
Option 1) Don't calculate it (I am not kidding).
Option 2) Quasi-harmonic (principle component) method from MD trajectory.
Yong
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Wei Chen
Sent: Thursday, August 04, 2005 11:04 AM
To: amber.scripps.edu
Subject: AMBER: nmode
Hi, Guys,
I have a big system about 10,000 atoms. I want to use mm_pbsa to calculate
free energy. But I have no enough memory for entropy calculation by nmode.
Does anybody have ideas to calculate entropy in different ways?
Thanks!
Wei Chen
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Received on Fri Aug 05 2005 - 01:53:01 PDT
