[gmx-users] Re: Preparation of the pure lipid system with charmm force field

[Justin A. Lemkul]

James Starlight wrote:
> Justin,
> 
> 
> So It seems that I've done all steps in accordance to that workflow  and 
> there have not been any more  errors during loading my system in the 
> gromp. :)
> 
> By the way I have some methodological questions
> 
> 1- Could you provide me with the source of the initial single lipids? 
> Previously I've done my system based on the VMD plugin for bilayer 
> constructing but I want to find single lipids and prepared my system 
> by-hands.
> 

Here are several:

http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources

> 2- Could you tell me other possible methods for self bi-layer 
> preparation starting from initial single lipid molecule ?
> 

Packmol is a program that can build bilayers.  You can also build crude 
monolayers with Gromacs that can be manipulated with genconf -nbox.  These would 
require significant equilibration, as they are artificially crystalline.

-Justin

> 
> Thanks again,
> 
> 
> James

-- 
========================================

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

========================================