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.
-Justin
Many thanks,
Richard
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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