[gmx-users] coarse grain in gromacs

Xavier Periole X.Periole at rug.nl
Mon Nov 24 10:32:09 CET 2008

On Sun, 23 Nov 2008 21:48:52 -0800
  BIN ZHANG <zhngbn at gmail.com> wrote:
> Hi, all:
>     Has anyone done the coarse graining using MARTINI force field?  
> Could you give me any suggestion on how to build a coarse grained  model 
>from the AA system? I checked the 
>website(http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html ) and it 
>seems to me they only provide a script for coarse graining  peptide. My AA 
>system will include protein+lipid+water.
The script indeed provides only transformation from AA to CG for proteins.
It should be soon available for any AA system.
In the mean time you can do it with a script of your own, choosing the
atoms from your AA file.

>     Thanks in advance.
> Bin
> -------------------------------------------------------------
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XAvier Periole - PhD

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

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