<div>Maybe there has been some mistake during your calculations? </div>
<div>No, g_covar gives the average covariance matrix. You can check this matrix with the command -ascii. <br>If you have used your own program to calculate entropy double check units conversion stuff. <br> </div>
<div>Regards.</div>
<div> </div>
<div>Pedro.</div>
<div> </div>
<div><span class="gmail_quote">2007/10/18, Naser, Md Abu <<a href="mailto:mn2@hw.ac.uk">mn2@hw.ac.uk</a>>:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div>
<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?<span class="q"><br><br>With regards,<br><br>Abu Naser<br><br>School Of Life Sciences<br>Heriot-Watt University
<br>Edinburgh EH14 4AS<br>Email: <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:mn2@hw.ac.uk" target="_blank">mn2@hw.ac.uk</a><br>Phone: +44(0)1314518265<br>Fax : +44(0) 131 451 3009<br><br><br><br>
<br><br><br></span>
<div><span class="e" id="q_115b3f29e56ad02d_2">-----Original Message-----<br>From: <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org
</a> 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 <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:mn2@hw.ac.uk" target="_blank">mn2@hw.ac.uk</a>>:<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: <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:mn2@hw.ac.uk" target="_blank">mn2@hw.ac.uk</a><br>> Phone: +44(0)1314518265
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