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-- 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/> On Fri, Feb 27, 2015 at 11:58 AM, Ross Walker <ross.rosswalker.co.uk> wrote: > Hi Joe > > Yes we are seeing the same thing. One thing you will see with the Monte > Carlo barostat is that the area per lipid you appear to get can be a > function of what you set the monte carlo test frequency (mcbarint) to be. > For now I think people just have to assume the Monte Carlo Barostat is > buyer beware until people have time to properly test it. I don't know how > extensively it was tested after adding to the code so there may be issues > there but as far as I can tell it is working properly so it may be a > methodological issue. > > Either way someone with more experience of the performance of different > pressure couplings in MD simulations can probably comment better than me > here. > > What we have found at least is if you use longer time intervals for the MC > barostat you appear to get better agreement with experiment - this is > encouraging to me. > > One thing that I don't think has been extensively tested is how well the > MC barostat does for systems far from equilibrium. I.e. if one uses the > berendsen barostat to equilibrate the area per lipid and then switches to > the MC barostat. Oh for the days when I used to have the time, and the > resources, to actually study such things indepth. :-( > > All the best > Ross > > > On Feb 27, 2015, at 8:29 AM, Joseph Baker <bakerj.tcnj.edu> wrote: > > > > Thanks Ross and Ian, > > > > Wanted to give an update on my lipid tests in case it is useful. Here are > > two figures for some POPE tests and a DOPC test. The POPE tests were done > > with either monte carlo barostat or berendsen barostat (indicated on > > figure). The two early tests that we did with a bad temperature for POPE > > and low hydration were obviously bad. The monte carlo barostat results > seem > > to come in a little low on the area per lipid for POPE compared to > > berendsen, but we're going to extend these a bit longer and see what > > happens out to 250 ns. > > > > I also included a figure for DOPC (following the Lipid14 tutorial exactly > > with Monte Carlo barostat), and you can see for DOPC the monte carlo > > barostat seems to do quite well compared to the Berendsen result for area > > per lipid from the Lipid 14 paper. > > > > 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/> > > > > On Fri, Feb 20, 2015 at 3:58 PM, Ross Walker <ross.rosswalker.co.uk> > wrote: > > > >> 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 | > >> --------------------------------------------------------- > >> > >> Note: Electronic Mail is not secure, has no guarantee of delivery, may > not > >> be read every day, and should not be used for urgent or sensitive > issues. > >> > >>> 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/> > >>> <area_per_lipid.jpg>_______________________________________________ > >>> AMBER mailing list > >>> AMBER.ambermd.org > >>> http://lists.ambermd.org/mailman/listinfo/amber > >> > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > >> > > <aplDOPC.jpg><aplPOPE.jpg>_______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Mar 10 2015 - 10:30:02 PDT