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

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 21 20:41:19 CEST 2011

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:


> 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.


> Thanks again,
> James


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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