[gmx-users] Re: Help regading Gromacs
Krzysztof Kuczera
kkuczera at ku.edu
Thu Sep 2 16:11:40 CEST 2010
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
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