[gmx-users] Virtual Sites in a polymer backbone

Broadbent, Richard richard.broadbent09 at imperial.ac.uk
Mon Oct 10 18:11:53 CEST 2011

I wish to keep certain parts of the backbone of my polymer rigid and planar,
as my primary interest is in the long length and timescale motion of the

I am attempting to utilise virtual sites as a means to keep aromatic groups
rigid and planar. My intention is to replace groups such as phenyl rings and
connected 5 and 6 member rings (similar to Phthalimide) with 3 reference
sites, then virtualise all the atomic sites. I'm going to use standard type
3 virtual sites and planned on constraining the relative positions of the 3
reference points. 

My plan is to pick sites such that the 3 eigenvalues of the moment of
inertia tensor, the centre of mass, and the total mass of the system are
conserved. As the system is two dimensional this amounts to a total of 6
non-linear equations for 9 variables which requires either additional
constraints or a physically motivated guess to solve.

I've searched the mailing list but have been unable to find any previous
attempts at this. I was wondering if anyone knew of a reference where this
had been attempted or if there had been any previous discussions about an
approach similar to this?

I am also very open to alternative approaches to holding these groups

Many thanks,


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