[gmx-users] define a new covalent bond in gromacs
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jan 5 22:57:32 CET 2010
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.
> 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.
>> spoel at xray.bmc.uu.se spoel at 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.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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