Re: [AMBER] Error Nmode entropy calculation

From: Nitin Sharma <>
Date: Mon, 13 Jan 2014 12:02:56 +0800

Thanks a lot :)

Nitin Sharma

-----Original Message-----
From: Jason Swails []
Sent: Friday, January 10, 2014 12:10 AM
Subject: Re: [AMBER] Error Nmode entropy calculation

On Thu, 2014-01-09 at 23:58 +0800, Nitin Sharma wrote:
> Thanks for the reply.
> Does this mean in order to use Normal mode analysis one should longer simulations so that system had properly equilibrated ?

You should never try to extract equilibrium properties from a system that has not properly equilibrated. If you don't have snapshots from proper Boltzmann sampling (and no way to reweight the snapshots to arrive rigorously at Boltzmann sampling), then computed thermodynamic properties will be wrong.

Normal mode analysis is not special here. It takes more snapshots to converge a quasi-harmonic entropy calculation, but in both cases you need to be 'equilibrated'.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sun Jan 12 2014 - 20:30:02 PST
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