Date: Fri, 20 Feb 2015 07:42:09 -0500
Hi all,
I've been having one of my students run some test simulations of a pure
POPE bilayer in pmemd.cuda with Amber14 using the Lipid14 force field. My
student has been following the protocol in the Lipid14 tutorial online.
Attached is a figure to show the current area per lipid vs time (in
picoseconds) we are getting (plotted are the steps from the beginning of
the series of Hold steps during which the box size equilibrates, and the
production phase).
I can explain why the green and red curves behave badly. For the green
curve my student accidentally only restrained half of the lipids during the
heating phase, we were also underhydrated (~ 26 waters/lipid instead of the
suggested 32/lipid in the Lipid14 paper for POPE), and we were running at
303 K (instead of 310 K as suggested for POPE in the Lipid14 paper). The
red curve represents a simulation where we fixed the restraints step during
heating, but were still underhydrated and at a lower T.
The black curve has appropriate hydration (enough waters in the system to
have at least 32 waters/lipid head), and we are now running at 310 K. It
seems that we are still getting a couple of angstrom^2 smaller area than is
reported in the Lipid14 paper however. I should note that our initial lipid
system was built using charmm-gui, it consists of 256 lipids instead of the
128 in the Lipid14 paper, and we are using the monte carlo barostat instead
of the Berendsen barostat for production (so the same as in the tutorial,
but different from what was done in the paper). My guess is that none of
these factors are resulting in us being a little low on the area per lipid
however.
Any suggestions would be appreciated! Thanks.
Joe
-- Joseph Baker, PhD Assistant Professor Department of Chemistry C101 Science Complex The College of New Jersey Ewing, NJ 08628 Phone: (609) 771-3173 Web: http://bakerj.pages.tcnj.edu/ <https://sites.google.com/site/bakercompchemlab/>
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(image/jpeg attachment: area_per_lipid.jpg)
