[gmx-users] Virtual Sites in a polymer backbone

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 10 19:07:36 CEST 2011

Broadbent, Richard wrote:
> 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
> polymer. 
> 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
> planar.

Any particular reason why improper dihedrals would not be suitable?  They are 
significantly easier to implement.


> Many thanks,
> Richard


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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