[gmx-users] qasi-harmonic entropy calculation
Pedro Alexandre de Araújo Gomes Lapido Loureiro
palaplou at gmail.com
Thu Oct 18 21:57:33 CEST 2007
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
2007/10/18, Naser, Md Abu <mn2 at hw.ac.uk>:
> 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
> 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
> calculate the entropy? Are you calculating it in dt time frames or are
> results cumulative? Why do you expect the entropy to decrease?
> 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
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> gmx-users mailing list gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users