# Re: [AMBER] Entropy: quasi harmonic vs NMode - Weird results

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 27 Dec 2011 12:18:24 -0500

They are completely different methods. Moreover, the quasi-harmonic
approximation converges very slowly as a function of the number of frames
you're using in your simulation. If you were to include more frames, you

Entropy is quite difficult to compute in general, so I'm really not too
surprised they're that far off. We've tested that ultra-low temperature
dynamics yields almost identical results for the two methods, but they may
easily diverge as the temperature rises.

HTH,
Jason

On Tue, Dec 27, 2011 at 10:57 AM, George Tzotzos <gtzotzos.me.com> wrote:

> I'm working on a 10ns (1000 frames) trajectory comprising of 5 sequential
> 2ns runs (200 frames each).
>
> Using the following input file
>
> &general
> endframe=1000, verbose=1,
> entropy=1,
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100,
> /
>
> I get
>
>
> -------------------------------------------------------------------------------
> ENTROPY RESULTS (QUASI-HARMONIC APPROXIMATION) CALCULATED WITH PTRAJ:
>
> Translational Rotational Vibrational
> Total
> Complex: 16.2644 16.2867 1324.9419 1357.4931
> Receptor: 16.2453 16.2793 1304.2450 1336.7695
> Ligand: 12.8458 10.7429 68.6309
> 92.2193
>
> DELTA S: -12.8267 -10.7355 -47.9339
> -71.4958
>
> -------------------------------------------------------------------------------
>
> Using:
>
> 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,
> /
>
> I get
>
> DELTA S total= -24.6088 +/- 1.6212
>
> Any suggestions as to the root of the discrepancy would be greatly
> appreciated.
>
> Regards
>
> George
>
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>

```--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Dec 27 2011 - 09:30:03 PST
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