Dear Jinyao,
If you are talking about making the ring rigid and side group rigid, I
would suggest adding a bunch of improper dihedrals to keep the
molecule rigid. I found without adding the improper dihedrals that
molecules that I would expect to be rigid were uncharacteristically
conformationally flexible. I hope that helps.
Best wishes,
Art Roberts
University of Washington
On Nov 11, 2008, at 7:25 PM, Jinyao Wang wrote:
gmx-users,
I am goning to carry out a rigid system system simulation for
Benzaldehyde. Atom charges,Bonds and Angles come from Gaussion03
computation. LJ interaction parameters come from oplsaa forcefield.
I don't know how to deal with rigid molecules in gromacs. So I
couldnot know how to write the .top file for the rigid Benzaldehyde.
If you could give me some suggest, It is appreciated.
Jinyao Wang
[EMAIL PROTECTED]
2008-11-12
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