Re: [AMBER] Entropy calculation of a molecule in water

From: case <>
Date: Wed, 15 Dec 2010 08:21:24 -0500

On Wed, Dec 15, 2010, Markus Kaukonen wrote:
> For testing purposes I'd like to calculate absolute entropy of a
> single molecule in water using amber11.
> Is this easily done by NAB or NMODE or ?

You can do this in the rigid-rotor harmonic oscillator (RRHO) approximation.
Either nmode or the nmode() function in NAB will provide this information.

[Note that most water models used in biomolecular simulation are rigid models,
and hence have no vibrational modes. nmode doesn't know this, and you would
just have to ignore the vibrational contribution to the entropy.]


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Received on Wed Dec 15 2010 - 05:30:02 PST
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