[gmx-users] Coarse graining for Benzene and related molecules

[ROHIT MALSHE]

Hi all, 

I want to simulate a molecule which has many benzene rings attached to each other. However I want to coarsegrain the system a lot !! 

I want to represent the center of masses of benzene rings with point masses. For all the parameters, such as bonds, angles, dihedrals I can use similar parameters as these are very rigid molecules but I am confused what Lennard Jones parameters should I use for these super atoms !

Can someone suggest how I can iteratively do that starting from a first guess ? 

Any suggestions are most welcome ! 


__________________________________________________________________________________________________________
Rohit Malshe                                                  1112, Engineering Hall       Tel :001 608 262 3370                                                             
Graduate Student                                            1415, Engineering Drive     Email: malshe at wisc.edu  
Chemical and Biological Engineering                  Madison, WI.                      
University of Wisconsin-Madison USA                 USA- 53726
__________________________________________________________________________________________________________