Hi Joe,
I think you are short on convergence here - 60ns is a little on the short side. We ran most of the lipids for 125ns in the lipid14 testing - and extended most out to 250ns. We also ran multiple repeats since there is often fluctuation in the time it takes a given lipid bilayer to equilibrate.
This was for systems half the size of yours so in your case equilibration will like take longer. So I'd take the black curve and run it 5x or so longer and see what you get.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Associate Research Professor |
| San Diego Supercomputer Center |
| Adjunct Associate Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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> On Feb 20, 2015, at 4:42 AM, Joseph Baker <bakerj.tcnj.edu> wrote:
>
> 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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Received on Fri Feb 20 2015 - 13:00:03 PST
