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

From: George Tzotzos <gtzotzos.me.com>
Date: Tue, 27 Dec 2011 16:57:39 +0100

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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Received on Tue Dec 27 2011 - 08:00:03 PST
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