[gmx-users] forcefield

[Tsjerk Wassenaar]

Dear Hadi,

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 <Mark.Abraham at anu.edu.au> 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
9747AG Groningen, The Netherlands
+31 50 363 4336
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