[gmx-users] Coarse graining for Benzene and related molecules
malshe at wisc.edu
Thu Apr 30 20:40:58 CEST 2009
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
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