[gmx-users] Discrepancy between Free Energy Perturbation usingGromos96 and OPLS

Sandeep Somani ssomani at bii.a-star.edu.sg
Thu Oct 13 09:03:15 CEST 2005

Thanks Erik and David. 
I compiled with the new toppush.c and reran the simulation. its fine

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Erik Lindahl
Sent: Thursday, October 13, 2005 6:12 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Discrepancy between Free Energy Perturbation
usingGromos96 and OPLS


On Oct 12, 2005, at 10:45 PM, David wrote:

On Wed, 2005-10-12 at 22:18 +0200, Erik Lindahl wrote:


A bug indeed. Fixed in both branches of CVS, and will be in a 3.3.1 
update in your near future.

In the meantime, you can download an updated src/kernel/toppush.c from


It's probably good to note that this is a bug in grompp rather than
mdrun and that it can be prevented (using manual labor) by writing the
Ryckaert-Bellemans parameters twice for each dihedral (such that A and B
state are identical).

Definitely - and you only need to do it for the handful of dihedrals
where the parameters are specified explicitly in the dihedrals topology
section, e.g. with a define string.



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