[gmx-users] Re: Help regading Gromacs

[Justin A. Lemkul]

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
> 
>  
> 
>  
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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