membrane protein md protocol

From: rob yang (
Date: Mon Jun 27 2005 - 10:36:15 CDT

i am trying to simulate glycophorin A dimeric helix in explicit lipid
bilayer membrane environment (say, POPC or DMPC). i know that the charmm
people have a standard protocol to set up md using CHARMM. i am just
wondering if the namd community has a standard protocol for such
simulations. i've tried to followed the tutorial provided by richard law
( but would like to
have a more systematic way of setting up the membrane and positioning the
helix dimer.
i also tried the gramicidin A tutorial
( which was
very helpful.
however, the lipid building step did not seem to use a pre-equilibrated
lipid library. could anybody give me a pointer to a more elaborated protocol
in setting up and running this type of simulation? thank you very much in

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