[gmx-users] define a new covalent bond in gromacs

[TJ Piggot]

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 
<spoel at 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.
>>> 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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----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.