[gmx-users] urey-bradley format

David van der Spoel spoel at xray.bmc.uu.se
Thu Sep 25 22:51:04 CEST 2008

Piotr Adam Pieniazek wrote:
> Hi,
> I'm trying to put in a Urey-Bradly type term into my force field, but 
> the format is not specified in the manual.
> atom_1 atom_2 atom_3  5  angle angle_force  bond bond_force
> I'm particularly confused about the last two terms. I've tried both 
> combinations and the results look reasonable in both cases.
Sorry for the confusion. The easy way to check is to run
gmxdump -s topol.tpr |more
then search for UR and check the parameter names and values.

> Thanks,
> Piotr
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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