How about using bond type 6 to restrain the distance without actually
creating a bond between the atoms?
Tom
--On Tuesday, January 05, 2010 22:57:32 +0100 David van der Spoel
<sp...@xray.bmc.uu.se> wrote:
Hans HEINDL wrote:
mdrun-openmm does not yet support any restraints
But gromacs does. Therefore, it seems you need to patch openmm, for which
you probably want to contact the openmm team.
Hans
Am Dienstag, den 05.01.2010, 22:12 +0100 schrieb David van der Spoel:
Hans HEINDL wrote:
Hi all,
I need to restrain the distance of two atoms in my system (the distance
is around 57 angstroms). As we plan to use mdrun-openmm which presently
does not support neither distance nor position restraints we need to
create a new covalent bond between the two atoms which would restrain
the distance of the two atoms. (This was Peter Eastmans idea from
Standford) How could we do that and where would be the best place to
define (I presume the *.top file) the bond and where should the bond
length and spring constant be defined?
Thanks in advance
Hans HEINDL
University of Westminster
London UK
How about normal distance restraints? Have you checked the manual?
--
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.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
--
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.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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----------------------
TJ Piggot
t.pig...@bristol.ac.uk
University of Bristol, UK.
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