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.k...@med.monash.edu.au
============================================
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