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 - 07:00:03 PDT
