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. Many thanks, Richard -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
