[gmx-users] membrane protein md using gromacs

rob yang nextgame at hotmail.com
Mon Jun 27 18:08:01 CEST 2005

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 gromacs 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 using gromacs? thank you 
very much in advance.

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