[gmx-users] Force constant for umbrella sampling potential

[Berk Hess]

Hi,

Gromacs has the half as a pre-factor in the potential.

Note that in 4.0.5 there is a g_wham program which can automatically
do the WHAM analysis on the mdrun output.

Berk

> Date: Tue, 1 Sep 2009 13:19:32 +0800
> From: mircial at sjtu.edu.cn
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Force constant for umbrella sampling potential
> 
> Hello everyone,
> 
> I would like to know does the harmonic biasing potential for running
> umbrella sampling in gromacs have a 0.5 in front or is the 0.5 term
> incorporated into the force constant value that we specify?
> On other words is the potential V=0.5*k(x-xo)^2 or V=k(x-xo)^2.
> 
> I am using Grossfield箂 WHAM
> algorithm and it assumes that the biasing potential used has a 0.5 in front,
> but I know for example CHARMM does not include the 0.5 and I just need to
> know if this is also the case with gromacs
> 
>   Thank you in advance.
> 
> R-X  Gu
> 
> 
> _______________________________________________
> 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

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090901/a93321d0/attachment.html>