In our PLoS Comput. Biol. study (Cojocaru et al 2011) with the GAFF
force field for POPC published by Jojart and Martinek we used surface
tension values ranging between 40 and 60 dyn/cm and found 50 and 60 to
provide reasonable lipid properties for the time of the simulations
(tens of ns) ... However, this was in NAMD and I don't know if the
surface tension is the same implemented in AMBER 12 and NAMD ..
I am curious about the references to the experimental values in Ross's
plots .. We tried to reproduce an experimental value of approx. 68 based
on a recent study (don't remember now the reference and I am traveling
right now)
Best,
Vlad
On 06/15/2012 11:26 AM, Ross Walker wrote:
> 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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--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Sat Jun 16 2012 - 00:30:02 PDT
