[gmx-users] Force constant for umbrella sampling potential

Berk Hess gmx3 at hotmail.com
Tue Sep 1 09:35:18 CEST 2009


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.


> 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
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