You also forgot to define "better". What do you want to learn from that peptide? Do you need all hydrogens for that? Or could you do without? Also consider that the generality of the question phrased does usually not trigger people in a way desired for reply. It sounds a bit like "I've got some homework, but would like you to do it for me". Study the manual and papers on MD, in particular of small peptides and force fields. Now there's a bit of homework ;)
Cheers,
Tsjerk
On 5/23/06, Mark Abraham <[EMAIL PROTECTED]> wrote:
hadi behzadi wrote:
> Hi all of users
>
> For HHAHHAADAAHHAAD peptide what kinde of force field is better ?
I don't know, but I could tell you the answer immediately for
HHAHAHADAAHHAAD peptide :-P
General force fields are parameterized to be reasonable over a range of
systems. The overview of force fields in the GROMACS manual is good, and
you should refer to the papers that describe them for more detail.
Mark
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--
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
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