[gmx-developers] Unusual virtual interaction sites

[Lee-Ping]

I did think about that.  My reasoning is a bit roundabout - my force
field parameterization strategy is to match the MM energies/forces to ab
initio calculations.  Thus, in the end there needs to be a force on the
physical atom.

When one has virtual sites, the forces are propagated from the virtual
site onto the host atom.  But when there are constraints, I don't think
this is the case.

- Lee-Ping

On Sat, 2011-05-07 at 15:29 -0400, chris.neale at utoronto.ca wrote:
> 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  
> constraints.
> 
> 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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> 
>