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

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 26 09:11:54 CEST 2005

> David.
> Dear David,
> No, this is not the same bug as the one I reported a couple of weeks 
> ago. This is a new one. I hope that the fix Berk implemented was in 
> runmd, more specifically in gmxlib/bondsfree.c
> What I am reporting now is a hidden mix-up of parameters in the tpr-file 
> due to grompp. It affects any free energy calculation in systems that 
> contain a heme group. I did not dig into the code myself this time, but 
> suggested two work-arounds in my previous mail. Please read it carefully.
Aha, I confused things, you reported the missing degrees to radian
conversion, wasn't it? Anyway, the bug mentioned above has been fixed in
grompp as well in the upcoming 3.3.1, as someone else had a similar

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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