[gmx-users] Brownian Dynamics - Tabulated Potential

[Jun Soo Kim]

Thank you very much for your reply. It is written in the manual and  
now I understand why.

Thanks,
Jun Soo

On Mar 11, 2010, at 11:04 AM, Berk Hess wrote:

> Hi,
>
> If you read the manual carefully, you would have noticed that the  
> potential
> is interpolated using cubic spline interpolation and the forces are  
> the derivative
> of these splines. Your scheme would work if the forces would be  
> interpolated linearly.
>
> Berk
>
> > From: junsookim76 at gmail.com
> > To: gmx-users at gromacs.org
> > Date: Thu, 11 Mar 2010 10:55:03 -0500
> > Subject: [gmx-users] Brownian Dynamics - Tabulated Potential
> >
> > Hi,
> >
> > I am trying the brownian dynamics simulations of a polymer chain  
> using
> > FENE potential and some effective potential. For this purpose, I  
> made
> > tabulated potentials for polymer bonds and non-bonded interactions,
> > and the simulations are running fine.
> >
> > As far as I know, the Brownian dynamics simulations only need the
> > forces at each time step (eq. 3.64 in Manual). So I tested the BD
> > simulation by setting the potential energy equal to Zero while  
> keeping
> > the force unchanged. Then I have a problem with simulations. The  
> bonds
> > are broken. I do not understand why we need the potential energy in
> > Brownian dynamics simulations. It would be really appreciated if
> > anyone provides any hint.
> >
> > Here is a piece of the bonding tabulated potential of FENE with the
> > potential set as zero and the force unchanged.
> >
> > Thanks,
> > Jun Soo
> >
> > # r	 U(r)	 -U'(r)	
> > 4.950 0.00000 11.5494
> > 4.952 0.00000 9.29470
> > 4.954 0.00000 7.10307
> > 4.956 0.00000 4.97242
> > 4.958 0.00000 2.90067
> > 4.960 0.00000 0.885859
> > 4.962 0.00000 -1.07395
> > 4.964 0.00000 -2.98060
> > 4.966 0.00000 -4.83590
> > 4.968 0.00000 -6.64158
> > 4.970 0.00000 -8.39931
> > 4.972 0.00000 -10.1107
> > 4.974 0.00000 -11.7774
> > 4.976 0.00000 -13.4008
> > 4.978 0.00000 -14.9825
> >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.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 gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> New Windows 7: Find the right PC for you. Learn more. --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.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 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...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100311/279eb0ff/attachment.html>