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

[David]

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
list.

> 
> Chris de Graaf and Chris Oostenbrink
> 
-- 
David.
________________________________________________________________________
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
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