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 |
> ---------------------------------------------------------
>
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Received on Fri Jun 15 2012 - 07:30:03 PDT
