[gmx-users] harmonic restraint with OpenMM

Jochen Hub jochen at xray.bmc.uu.se
Sat Feb 5 07:55:13 CET 2011


I am trying to restrain an ion that is coordinated by a few protein 
atoms, to avoid that the ion might fly off. The simulation should be run 
on a GPU (with OpenMM) and implicit solvent. First I tried to restrain 
the ion using bonds of type 6, but harmonic potentials are not supported 
by OpenMM. Turning the restraint into a normal bond (type 1) would be 
fine since I only constrain bond lengths of hydrogens. However, that 
gives a grompp error,

"Cannot find length for atoms 386-2262 involved in angle"

meaning that the function find_gb_bondlength in topio.c does not find a 
bond length for the ion-protein atom bond, although the bond length is 
clearly defined in the topology.

I am a bit stuck now. Does anyone know how one could introduce some kind 
of distance restraint with OpenMM and implicit solvent?

I am using gmx 4.5.3 and OpenMM 2.0.

Thanks a lot,


Dr. Jochen Hub
Computational and Systems Biology
Dept. of Cell&  Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4715056 Fax: +46-18-511755

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