[gmx-users] coarse grain in gromacs

[Xavier Periole]

On Mon, 24 Nov 2008 22:28:36 -0500
  "Justin A. Lemkul" <jalemkul at vt.edu> wrote:
> 
> 
> 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?
I've done this quite a lot and never got any complain! Have a look at
the box size may be!

Note also that when using the CG you have to specify the vdW radius used
to place the water molecules. A value of 0.197 gives a quite good starting
conformation: no big deformation of the box.

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

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