Chih-Ying Lin wrote:
Hi
the molecular structure : bond length, bond angle, dihedral angle ....
the bond length, bond angle are easily determined..
but the dihedral angle are hard to control...
Are you looking to control (i.e., restrain/constrain) these parameters, or
measure them?
with one set of the force field parameter, I could not get the exact
structure of the molecule (not all of the dihedral angles are the
same , but bond length and bond angle are the same)
I should think not! All bonds are not created equal. Maybe I'm just missing
your meaning. Are you missing a parameter for your molecule? If so, you'll
have to derive it, or at least use a comparable parameter. Are you trying to
make a measurement? If so, you haven't provided enough information to get a
very helpful reply.
will it affect my rest of simulation severely?
Depends on how you answer the above :)
-Justin
Thanks
Lin
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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