[gmx-users] coarse grain in gromacs

[Justin A. Lemkul]

BIN ZHANG wrote:
> 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?

I've used genbox with a simple CG system, no problem.  Does you genbox function 
normally for atomistic systems?

-Justin

>      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.
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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