Maybe there has been some mistake during your calculations? No, g_covar gives the average covariance matrix. You can check this matrix with the command -ascii. If you have used your own program to calculate entropy double check units conversion stuff.
Regards. Pedro. 2007/10/18, Naser, Md Abu <[EMAIL PROTECTED]>: > > 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: [EMAIL PROTECTED] > Phone: +44(0)1314518265 > Fax : +44(0) 131 451 3009 > > > > > > > -----Original Message----- > From: [EMAIL PROTECTED] 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 <[EMAIL PROTECTED]>: > > > > 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: [EMAIL PROTECTED] > > Phone: +44(0)1314518265 > > Fax : +44(0) 131 451 3009 > > > > > > > > > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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