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
would get a different answer.
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
