[gmx-users] hydrocarbon force fields
jake at ncsa.uiuc.edu
Wed Sep 20 13:37:20 CEST 2006
For hydrocarbon force fields, see:
Chiu, S. W., Clark, M. M., Jakobsson, E.,
Subramaniam, S., and H. L. Scott. 1999b.
Optimizations of hydrocarbon chain interaction
parameters: Application to the simulation of
fluid phase lipid bilayers. J. Phys. Chem. B 103:6323-6327
At 09:47 PM 9/19/2006, you wrote:
>Ö÷ÔÂ £º£© wrote:
> > ¡·Has this force field been demonstrated to be effective >for this sort of
> > >simulation? If not, maybe you've begun to demonstrate >that it isn't?
> > >Mark
> > Yes , you are quite right. In GMX manual 3.2, at the end of chapter 4,
> > it was said that gromos96 is not, however, recommended for use with long
> > alkanes and lipids.
> > So user has to validate force parameters. Now the problem is for a
> > periodic boundary system, the density is ok but the Rg is too small. I
> > feel the parameters for proper dihedrals need to be improved. Is it right?
>It's likely that nobody knows.
>Find a force field that does work for such simulations, or read
>everything you can find on how to build force fields and do it from
>scratch. Modifying one sort of parameter is like taking a Beethoven
>symphony and substituting the second violin part with bass guitar line
>from "Smoke on the Water". It might work, but you'd be mad to bet on it.
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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and
Integrative Physiology, and of Biochemistry, and
of the Center for Biophysics and Computational Biology
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
3261 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896 fax 217-244-2909
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