[gmx-users] Virtual Sites in a polymer backbone
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 listgmx-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
Re: [gmx-users] Virtual Sites in a polymer backbone
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 -- gmx-users mailing listgmx-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
Re: [gmx-users] Virtual Sites in a polymer backbone
Any particular reason why improper dihedrals would not be suitable? They are significantly easier to implement. Yes the force field parameters for the molecule are not known and I am therefore fitting the parameters to Density Functional Theory. If I allow the units to move out of plane even slightly their will be additional parameters to fit which will make the problem unfeasibly computationally expensive. Thank you for the suggestion, Richard -- gmx-users mailing listgmx-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
