[gmx-users] how to write .top file for a rigid molecule

Arthur Roberts aroberts99163 at yahoo.com
Wed Nov 12 09:27:41 CET 2008

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
>         wangjy at ciac.jl.cn
>           2008-11-12
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