From: rob yang (nextgame_at_hotmail.com)
Date: Mon Jun 27 2005 - 10:36:15 CDT
hi,
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
(http://mccammon.ucsd.edu/~rlaw/ctbp_workshop_rlaw.htm) 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
(http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/) 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
advance.
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