AMBER Archive (2005)

Subject: RE: AMBER: nmode

From: Yong Duan (duan_at_ucdavis.edu)
Date: Thu Aug 04 2005 - 19:03:26 CDT

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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Wei Chen
Sent: Thursday, August 04, 2005 11:04 AM
To: amber_at_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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