From: Keith Battle (keith.battle_at_gmail.com)
Date: Tue Jul 20 2010 - 15:52:30 CDT
Hi NAMD users,
Has anyone been able to simulate a residue based coarse grain system
including all atom species? I have heard of other programs that will do so,
but can't find any literature on NAMD capabilities. Currently, I use the CG
plugin in VMD to build my systems but I don't see an option to incorporate
all atoms. Ideally, I would like to simulate a coarse grained protein in
coarse grained water with all atom ions such as phosphates, calciums, and
hydroxides. This would allow me to parameterize the force field such that
the ions would have the best ability to form a crystal. Any help would be
appreciated.
Best,
Keith Battle
University of South Alabama
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