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