[gmx-users] Which POPC Bilayer to start?
akshay17 at olemiss.edu
Wed Sep 20 23:51:17 CEST 2006
I am trying to use POPC bilayer for doing GPCR simulation.
I have come across two options of generating a POPC bilayer >>>>
1. I can generate a POPC bilayer from the VMD Membrane plug-in, wherein the
membrane is generated from the pre-built membrane square patches and lipid
tails are (almost) fully extended.
2. Alternatively, I can download the pre-equilibrated POPC bilayer from Dr.
Tieleman's website, http://moose.bio.ucalgary.ca/index.php?page=People
Since, I am new to the GPCR-membrane modeling, can you suggest me which out
of the above two options can be a better starting point for the simulation
of my GPCR protein? A membrane generated from VMD or a pre-equilibrated
membrane?? Would the equilibration time for my protein be lesser in one out
of the two?
If option 2 is a good idea then out of popc128a.pdb and popc128b.pdb (both
available from Prof. Tieleman's website), which will be a better model to
Thank you very much in advance.
Graduate Research Assistant
Faser Hall 417, Department of Medicinal Chemistry Research Institute of
Pharmaceutical Sciences University of Mississippi University, MS 38677
E-mail: akshay17 at olemiss.edu
Tel: 662-915-1286 (office); Web: www.olemiss.edu
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