[gmx-users] qasi-harmonic entropy calculation

[Naser, Md Abu]

Hi Pedro,

I am using 4565.9 as a conversion factor. I dont see any problem unless  any condtion I needed to 
satisfy during the simulation. Simulation gave the result what I had expected.
 
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 8:57 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] qasi-harmonic entropy calculation
 
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 <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
>
> 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 <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
> >
> >
> >
> >
> >
> > _______________________________________________
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