[gmx-developers] Unusual virtual interaction sites

Lee-Ping leeping at MIT.EDU
Sat May 7 19:20:57 CEST 2011

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?


- Lee-Ping

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