[gmx-developers] Unusual virtual interaction sites

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat May 7 21:29:52 CEST 2011

why do they need to be virtual sites? you could do this with regular  
atoms with zero LJ terms and define the geometry by a set of  

Quoting Lee-Ping <leeping at MIT.EDU>:

> Dear all,
> I've been randomly thinking of a new type of model for elemental
> materials and alloys in which individual atoms can be described using
> several virtual sites.  For example, consider a metal ion with six
> virtual sites that allows it to coordinate water in an octahedral
> geometry.  It would allow for bonds to be broken and formed without
> explicit topology definitions or bond-order potentials.
> I am wondering if it's possible at all to have such a force field with
> Gromacs.  It does seem like all of the virtual sites are defined with
> respect to 2 atoms or more, which is reasonable - conceptually I don't
> see how I can uniquely attach a virtual site to only one atom.  Has
> anyone considered this problem before?
> Thanks!
> - Lee-Ping
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