[gmx-users] Coarse graining for Benzene and related molecules
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 30 20:48:09 CEST 2009
ROHIT MALSHE wrote:
> 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
The best advice for developing parameters (for any type of system) is to read
relevant literature, decide on a derivation scheme, and set to work. There is
no substitute for doing your own homework!
> 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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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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