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<P><FONT SIZE=2>Hi Pedro,<BR>
<BR>
I am using 4565.9 as a conversion factor. I dont see any problem unless any condtion I needed to<BR>
satisfy during the simulation. Simulation gave the result what I had expected.<BR>
<BR>
With regards,<BR>
<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 8:57 PM<BR>
To: Discussion list for GROMACS users<BR>
Subject: Re: [gmx-users] qasi-harmonic entropy calculation<BR>
<BR>
Maybe there has been some mistake during your calculations?<BR>
No, g_covar gives the average covariance matrix. You can check this matrix<BR>
with the command -ascii.<BR>
If you have used your own program to calculate entropy double check units<BR>
conversion stuff.<BR>
<BR>
Regards.<BR>
<BR>
Pedro.<BR>
<BR>
2007/10/18, Naser, Md Abu <mn2@hw.ac.uk>:<BR>
><BR>
> Hi Pedro,<BR>
><BR>
> Thank you for your attention to my email. Yes, I am using Schlitter<BR>
> equation and the<BR>
> rusult is cumulative. The entropy is meant to be decreased as the protein<BR>
> is stick<BR>
> on to a surface.<BR>
><BR>
> I have used the entire protein as a subset. Is the programme takes the<BR>
> 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<BR>
> 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<BR>
> to<BR>
> calculate the entropy? Are you calculating it in dt time frames or are<BR>
> 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>
> > _______________________________________________<BR>
> > gmx-users mailing list gmx-users@gromacs.org<BR>
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