From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Thu Jul 05 2018 - 08:03:31 CDT
Hi Kelly,
there is a membrane-protein tutorial that you can follow at
http://www.ks.uiuc.edu/Training/Tutorials/#memprot. NAMD does not detect
the axis of the membrane in any simulation. The important step here is to
define the periodic boundary conditions to ensure that the membrane is
"infinite", so right at the pbc limits, and you don't get water in the
hydrophobic region
of the membrane
. All these steps are taken care during the structure preparation in VMD
(see tutorial)
and in the definition of the pbc in the configuration files of NAMD.
Additional options might be useful such as useConstantRatio
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