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<P><FONT SIZE=2>Hi Pedro,<BR>
<BR>
Thank you for your attention to my email. Yes, I am using Schlitter equation and the<BR>
rusult is cumulative. The entropy is meant to be decreased as the protein is stick<BR>
on to a surface.<BR>
<BR>
I have used the entire protein as a subset. Is the programme takes the final structure<BR>
for calculating covariance?<BR>
<BR>
With regards,<BR>
<BR>
Abu Naser<BR>
<BR>
School Of Life Sciences<BR>
Heriot-Watt University<BR>
Edinburgh EH14 4AS<BR>
Email: mn2@hw.ac.uk<BR>
Phone: +44(0)1314518265<BR>
Fax : +44(0) 131 451 3009<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: gmx-users-bounces@gromacs.org on behalf of Pedro Alexandre de Araújo Gomes Lapido Loureiro<BR>
Sent: Thu 18/10/2007 1:47 PM<BR>
To: Discussion list for GROMACS users<BR>
Subject: Re: [gmx-users] qasi-harmonic entropy calculation<BR>
<BR>
Hi,<BR>
<BR>
I understand you are using the Schlitter equation, is that so?<BR>
Could you give more details? Such as, what subset of atoms are you using to<BR>
calculate the entropy? Are you calculating it in dt time frames or are your<BR>
results cumulative? Why do you expect the entropy to decrease?<BR>
<BR>
Regards,<BR>
<BR>
Pedro.<BR>
<BR>
<BR>
2007/10/18, Naser, Md Abu <mn2@hw.ac.uk>:<BR>
><BR>
> Hi all user,<BR>
><BR>
> I have calculated entroy over time from eigenvalue(g_covar) and<BR>
> the result shows that the entropy decreasing towards zeo. The results<BR>
> is ok as far as it decreases. But I do not understand why it is<BR>
> approaching<BR>
> to zero towards the end of the simulation. Can anyone explain why?<BR>
><BR>
> I would appreciate your response.<BR>
><BR>
><BR>
> With regards,<BR>
> Abu Naser<BR>
><BR>
> School Of Life Sciences<BR>
> Heriot-Watt University<BR>
> Edinburgh EH14 4AS<BR>
> Email: mn2@hw.ac.uk<BR>
> Phone: +44(0)1314518265<BR>
> Fax : +44(0) 131 451 3009<BR>
><BR>
><BR>
><BR>
><BR>
><BR>
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