[gmx-users] Simulation of only Lipid Bilayer

[Itamar Kass]

Hi Saumya,

for topology please look at those two paper from Poger in which he 
derive new parameters for various lipids:

1. Poger D., van Gunsteren W. F. & Mark A. E. (2009) A new force field 
for simulating phosphatidylcholine bilayers. J. Comput. Chem. in press 
(doi: 10.1002/jcc.21396)

2. Poger D. & Mark A. E. (2010) On the validation of molecular dynamics 
simulations of saturated and cis-monounsaturated phosphatidylcholine 
lipid bilayers: a comparison with experiment. J. Chem. Theory Comput. 6, 
325-336

A nice site to find coordinates for well equilibrated lipids is the one 
of Peter Tieleman 
<http://moose.bio.ucalgary.ca/index.php?page=Peter_Tieleman> 
(http://moose.bio.ucalgary.ca/).

Good luck with the simulations,
Itamar


On 6/04/10 9:35 PM, Justin A. Lemkul wrote:
>
>
> 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.
>
> -Justin
>
>> 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
>>
>

-- 


"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut

===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at med.monash.edu.au
============================================

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