Virtual Sites for Organohalogens

The functionality of OpenMM will (eventually) include everything that one would need to run modern molecular simulation.
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Christopher Rowley
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Joined: Mon Apr 27, 2009 7:25 am

Virtual Sites for Organohalogens

Post by Christopher Rowley » Thu Jun 12, 2014 12:24 pm

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
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Peter Eastman
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Joined: Thu Aug 09, 2007 1:25 pm

Re: Virtual Sites for Organohalogens

Post by Peter Eastman » Thu Jun 12, 2014 1:00 pm

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
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