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

Xavier Periole X.Periole at rug.nl
Fri May 1 09:16:18 CEST 2009

On Thu, 30 Apr 2009 13:40:58 -0500
  ROHIT MALSHE <malshe at wisc.edu> 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 !! 
Did you look at the Martini CG force field. It should be help full.
You can google it.
> 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, 
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> University of Wisconsin-Madison USA                 USA- 53726
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XAvier Periole - PhD

- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands

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