[gmx-users] Bug in free energy calculations in heme-containing systems

David spoel at xray.bmc.uu.se
Tue Oct 25 18:51:19 CEST 2005

On Tue, 2005-10-25 at 18:00 +0200, Chris Oostenbrink wrote:

> Solution
> The reason for all this probably lies in grompp, where the standard 
> force-field parameters are incorporated into the system topology, 
> resulting in a faulty tpr-file. In the case where the Heme group is not 
> coordinated to a His, commenting out the default force-field parameters 
> in file ffG43a1bon.itp seems to help. Otherwise, explicitly stating all 
> Heme parameters in state B as well may also prevent the error from 
> happening.

Since you reported this previously it has been discussed on one of the
mailing lists. Berk Hess has implemented a fix for this behavior in
grompp which will be in 3.3.1. Check the discussion on the gmx-revision

> Chris de Graaf and Chris Oostenbrink
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-users mailing list