Re: [AMBER] Entropy: nmode and quasi-harmonic approximation

From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
Date: Tue, 24 Apr 2012 10:58:16 +0100

On Tue, 24 Apr 2012 11:24:15 +0200
George Tzotzos <gtzotzos.me.com> wrote:

> I've run entropy calculations on exactly the same system with nmode
> and quasi-harmonic approximation.
>
> The results are baffling to say the least (see below). I would be
> grateful for any suggestions as to why there's such a huge
> discrepancy.

Global motions converge slowly and thus obtaining reliable entropies
from QHA is a quite challenging task. How large is your system? How
long have you simulated? What atoms have you included in your
analysis? Have you looked at the PCA modes? How many sample points do
you have in your trajectory? I think you need at least 3N points (N =
number of atoms) to get all modes.

Cheers,
Hannes.

> Best regards
>
> George
>
> Input file for running PB and GB
> |&general
> | interval=4, endframe=1000, verbose=1,
> | entropy=1,
> |/
> |&gb
> | igb=2, saltcon=0.100
> |/
> |&pb
> | istrng=0.100,
> |/
>
> ENTROPY RESULTS (QUASI-HARMONIC APPROXIMATION) CALCULATED WITH PTRAJ:
>
> Translational Rotational
> Vibrational Total DELTA S: -12.8267
> -10.7349 -62.7713 -86.3326
>
> DELTA G binding = -40.8873 +/-
> 2.6499 0.1676
>
>
>
> Input file for running entropy calculations using NMode
> |&general
> | endframe=1000, keep_files=2,
> |/
> |&nmode
> | nmstartframe=10, nmendframe=910,
> | nminterval=100, nmode_igb=1, nmode_istrng=0.1,
> |/
>
> ENTROPY RESULTS (HARMONIC APPROXIMATION) CALCULATED WITH NMODE:
>
> DELTA S total= -24.6088 +/- 1.6212
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Received on Tue Apr 24 2012 - 03:30:04 PDT
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