[gmx-users] qasi-harmonic entropy calculation

[Naser, Md Abu]

Hi Pedro,

Thank you for your attention to my email. Yes, I am using Schlitter equation and the 
rusult is cumulative. The entropy is meant to be decreased as the protein is stick 
on to a surface.

I have used the entire protein as a subset. Is the programme takes the final structure 
for calculating covariance? 
 
With regards,

Abu Naser 

School Of Life Sciences 
Heriot-Watt University 
Edinburgh EH14 4AS 
Email: mn2 at hw.ac.uk
Phone: +44(0)1314518265 
Fax : +44(0) 131 451 3009 


 



-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Pedro Alexandre de Araújo Gomes Lapido Loureiro
Sent: Thu 18/10/2007 1:47 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] qasi-harmonic entropy calculation
 
Hi,

I understand you are using the Schlitter equation, is that so?
Could you give more details? Such as, what subset of atoms are you using to
calculate the entropy? Are you calculating it in dt time frames or are your
results cumulative? Why do you expect the entropy to decrease?

Regards,

Pedro.


2007/10/18, Naser, Md Abu <mn2 at hw.ac.uk>:
>
>  Hi all user,
>
> I have calculated entroy over time from eigenvalue(g_covar) and
> the result shows that the entropy decreasing towards zeo. The results
> is ok as far as it decreases. But I do not understand why it is
> approaching
> to zero towards the end of the simulation. Can anyone explain why?
>
> I would appreciate your response.
>
>
> With regards,
> Abu Naser
>
> School Of Life Sciences
> Heriot-Watt University
> Edinburgh EH14 4AS
> Email: mn2 at hw.ac.uk
> Phone: +44(0)1314518265
> Fax : +44(0) 131 451 3009
>
>
>
>
>
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