Many thanks Hannes,
The corollary from your answer is that the system is far from convergence.
I'm rather naive on QHA and if you can point out to me any appropriate literature, I would be most grateful. I didn't find anything in the manual. Perhaps I didn't look hard enough.
My system has 125 residues. Production MD was 10ns (1000 frames). I used an interval of 4, therefore 250 frames were read. I did not look at the PCA modes.
Best regards
George
On Apr 24, 2012, at 11:58 AM, Hannes Loeffler wrote:
> 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 - 05:00:04 PDT
