AMBER Archive (2008)

Subject: Re: AMBER: Nmode entropy calcs

From: David A. Case (case_at_scripps.edu)
Date: Sun Jul 13 2008 - 10:45:56 CDT

On Sat, Jul 12, 2008, Sergio Wong wrote:
>
> Could anyone point me to literature explaining how Nmode is used to
> calculate translational and rotational entropy?? It would also be nice to
> have a reference for the vibrational entropy routines. I use Nmode as part
> of the MM-PBSA analysis in Amber 9.

Nmode uses the RRHO (rigid-rotor, harmonic oscillator) approximation to
compute thermodynamics. The relevant formulas are given in virtually any
physical chemistry textbook (that covers statistical mechanics). McQuarrie's
books (either Statistical Thermodynamics or Statistical Mechanics) have
particularly clear explanations.

...dac

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