Hello Marek,
We have not tried other solvent models with the current lipid force field parameters, yet. It's definitely something to look at. Also, it is crucial in lipid simulations to have a properly solvated bilayer system (E.G. at least a minimum number of water molecules per lipid).
Ben
________________________________________
From: Marek Maly [marek.maly.ujep.cz]
Sent: Saturday, June 16, 2012 3:19 AM
To: AMBER Mailing List
Subject: Re: [AMBER] R: R: strange POPC under lipids 11 FF
Thanks Ross !
I had also the additional question regarding the lipids you are testing,
but I
found the answer in this recent contribution in Amber forum:
http://archive.ambermd.org/201205/0340.html
which also confirms your information about the "hot" paper in revision.
So thanks a lot for this great work and let's keep fingers crossed !
Best wishes,
Marek
Dne Sat, 16 Jun 2012 00:43:30 +0200 Ross Walker <ross.rosswalker.co.uk>
napsal/-a:
> 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,
>> may
>> > not
>> > be read every day, and should not be used for urgent or sensitive
>> issues.
>> >
>> >
>> >
>> >
>> >
>> >
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