[gmx-users] Simulation of only Lipid Bilayer

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 6 13:35:19 CEST 2010

Arun kumar V wrote:
> Try PRODRG server to build the molecule as well as to get topology file. 
> Though  you might have to be careful in using this topology file.

If by "be careful" you mean "don't use this topology," I'll agree :)  The Gromos 
parameters for lipids (at least Gromos87 and Gromos96 43a1, given by PRODRG) 
fall far short of reproducing lipid properties.  That, and the charges assigned 
by PRODRG for lipids will not resemble any known parameter set, requiring a 
complete re-write of this topology.  You could use PRODRG to build the molecule, 
but there are a number of other programs that can do that as well (see the 
Gromacs site for a list).

To the original post: What lipid are you looking to simulate?  Many 
pre-equilibrated lipid bilayers are available in the public domain, along with 
suitable paramters, saving you a lot of work in building these systems.  They 
can be tricky.


> Arun
> Saumya wrote:
>> Hi all,
>> Well, I have been trying to make lipid bilayers using genconf of
>> gromacs from a single lipid molecule.
>> Can anyone tell me how to proceed with the simulation of lipid
>> bilayers starting with a single lipid molecule?
>> How can I obtain the .pdb file for a lipid?
>> Is there any manual that describes the procedure using Gromacs?
>> Hoping for some inputs.
>> Regards
>> Saumya


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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