[gmx-users] Discrepancy between Free Energy Perturbation using Gromos96 and OPLS

Erik Lindahl lindahl at sbc.su.se
Thu Oct 13 00:11:54 CEST 2005


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

> On Wed, 2005-10-12 at 22:18 +0200, Erik Lindahl wrote:
>> Hi,
>> 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
>> ftp://ftp.gromacs.org/pub/tmp/toppush.c
> 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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