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.
Do you define "rigid" as "containing constrained bonds"? You should be able to
choose appropriate bonded parameters from ffoplsaabon.itp, but in the .top all
you would have to specify are the atom numbers involved in the bond; as long as
there are parameters for that particular bond, they will be read from
ffoplsaabon.itp.
-Justin
Jinyao Wang
[EMAIL PROTECTED]
2008-11-12
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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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