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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Received on Sat Jun 16 2012 - 03:30:05 PDT
