[gmx-users] Re: Help regading Gromacs

[Krzysztof Kuczera]

  For building membrane/protein systems I recommend charmm-gui.org
The server automatically builds the coordinates, which you should be 
able to use
with any modeling program;   CHARMM equilibration scripts are generated 
as well

Krzysztof

On 9/2/10 6:20 AM, Justin A. Lemkul wrote:
>
> Please keep all Gromacs-related correspondence on the gmx-users list.  
> I am not a private help service.  I am CC'ing the message there; 
> please continue any discussion via the forum.
>
> Creating a lipid bilayer is not a particularly easy task.  You can 
> generate a leaflet by replicating the coordinates of one lipid 
> molecule in the x-y plane using genbox, then create the facing leaflet 
> by rotating the existing leaflet using editconf.  Concatenate the 
> files and you have yourself a bilayer (which will need extensive 
> equilibration, of course).  Adding water is trivial with genbox.
>
> -Justin
>
> praba vathy wrote:
>> Dear Sir,
>>
>> I want to create a lipid bilayer in which protein is inserted and on
>>
>> the top of insertion i need to put the water molecules and then at the
>>
>> bottom as well. I don't understand  that how to place the
>>
>> molecules  using Gromacs. Please give suggestions.
>>
>>
>>
>>
>>
>>
>> Regards,
>> Prabha. K
>>
>>
>>
>>
>>
>


-- 
Krzysztof Kuczera
Professor
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html