simtk.org

Hi,

I'm interested in using openmm to simulate organohalogen molecules where there is a virtual site attached to the halogen, collinear to the C-X bond (J. Chem. Theory Comput., 2012, 8 (10), pp 3895–3901 http://dx.doi.org/10.1021/ct300180w). I'm not sure if any of the VirtualSite types currently support this. Could something like a TwoParticleAverageSite with a negative weight on the halogen atom work?

Thanks,
Chris

A negative weight is fine, so you can definitely use that to position the site in line with the two atoms. Is the distance between the atoms constrained? If not, the distance to the virtual site will vary.

OpenMM 6.1 will also add an new, very flexible type of virtual site called LocalCoordinatesSite. See https://github.com/SimTk/openmm/blob/ma ... tualSite.h.

Peter