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

[Justin A. Lemkul]

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!

-Justin

> 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
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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