Re: [AMBER] Error Nmode entropy calculation

From: Jason Swails <>
Date: Thu, 09 Jan 2014 11:10:22 -0500

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 Thu Jan 09 2014 - 08:30:02 PST
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