[gmx-users] coarse grain in gromacs

[BIN ZHANG]

Hi,:
      Is it possible to solvate the system using coarse grained water  
molecule?
      I tried command: genbox -cp cg_protein.pdb -cs cgwat.pdb -o  
cg_protein_water.pdb, but get Segmentation fault.
      Can anyone give me some suggestion or basic procedure to build a  
coarse grained system?
      Thanks in advance.
Bin


On Nov 24, 2008, at 1:32 AM, Xavier Periole wrote:

> 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.
>
> XAvier
>>    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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-------------------------------------------------------------
The tree of liberty must be refreshed from time to time with the blood  
of patriots and tyrants.