Ref: (70) Kučerka, N.; Nieh, M.-P.; Katsaras, J. Biochim. Biopys. Acta 2011, 1808, 2761–2771.
Issue with surface tension: Mostly due to VDW terms and dihedrals in the aliphatic tails. We have a paper in revision right now that solves this so one does not need constant surface tension. We will incorporate this into Lipid11 making Lipid12 (or maybe 13) shortly.
I don't think the water model has too much effect since the area per lipid is most affected by the interaction of the tails.
Giovani, Y axis is Area per lipid in Angstroms squared. Sorry that got cutoff when I pulled out the figure.
All the best
Ross
> -----Original Message-----
> From: Marek Maly [mailto:marek.maly.ujep.cz]
> Sent: Friday, June 15, 2012 7:05 AM
> To: 'AMBER Mailing List'
> Subject: Re: [AMBER] R: R: strange POPC under lipids 11 FF
>
> Hi all,
> just to ammend Giovanni's last question, Ross could you
> sent the reference for the experimental data you are using in your
> actual
> study ?
>
> Regarding to insufficient ability of the lipid ff to reproduce some
> experimental data
> unless artificial external surface_tension is applied might it be also
> partially connected
> with limited accuracy of the simplest water parametrization used -
> TIP3P
> ? as the hydrophobic/filic
> effects play here important role.
>
> Of course it could be eventually easily tested by comparing to
> simulations
> with another water models (SPC ...)
>
> Best wishes,
>
> Marek
>
>
>
>
>
>
> Dne Fri, 15 Jun 2012 15:41:53 +0200 Giovanni Pavan
> <giovanni.pavan.supsi.ch> napsal/-a:
>
> > Dear Ross and dear Åge,
> >
> > Thanks a lot for the useful infos.
> > Just an additional question for Ross:
> > I am not sure I got correctly what are the numbers at the Y axis in
> the
> > picture you have sent me (X axis is simulation time).
> > Best
> >
> > Giovanni
> >
> > Dr. Giovanni M. Pavan
> >
> > Laboratory of Applied Mathematics and Physics (LaMFI)
> > University of Applied Sciences of Southern Switzerland (SUPSI)
> > Centro Galleria 2, Manno 6928, Switzerland.
> > e-mail: giovanni.pavan.supsi.ch
> > web: http://www.dti.supsi.ch/~pavan/
> > skype: giovanni_pavan
> > phone: +41 58 666 65 60
> >
> >
> > -----Messaggio originale-----
> > Da: Ross Walker [mailto:ross.rosswalker.co.uk]
> > Inviato: venerdì, 15. giugno 2012 11:26
> > A: giovanni.pavan.supsi.ch; 'AMBER Mailing List'
> > Oggetto: Re: [AMBER] R: strange POPC under lipids 11 FF
> >
> > Hi Giovanni,
> >
> >> is there any reference regarding the use of gamma_ten=17 as a
> reliable
> >> value for surface tension?
> >> Because for instance I found out this paper:
> >> http://onlinelibrary.wiley.com/doi/10.1002/jcc.20748/abstract
> >> where they say that for POPC parametrized with the .gaff force field
> >> work pretty well if surface tension is set to 60 mN/m.
> >> I guess however that it depends on the different parametrization
> >> performed by gaff.
> >
> > We are in the process of trying to get a manuscript describing the
> Lipid
> > 11
> > force field published. Unfortunately as you might imagine given the
> > competition in simulating lipids we are encountered a little bit of
> > animosity which is unfortunately delaying publication.
> >
> > The value you quote is for using the GAFF force field. It is also
> highly
> > dependent on specifically which atom types were chosen, not everybody
> > chooses the same atom types consistently when using GAFF for lipids.
> They
> > also don't always calculate the charges in a consistent way. Thus the
> > value
> > you need varies by implementation. For the current version of the
> Lipid
> > 11
> > force field (released with AMBER 12) we have found a value of 17
> tends
> > to be
> > optimal for POPC. See the attached plot.
> >
> > All the best
> > Ross
> >
> >
> > /\
> > \/
> > |\oss Walker
> >
> > ---------------------------------------------------------
> > | Assistant Research Professor |
> > | San Diego Supercomputer Center |
> > | Adjunct Assistant 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,
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> >
> >
> >
> >
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Received on Fri Jun 15 2012 - 16:00:05 PDT
