[gmx-developers] Re: gmx-developers digest, Vol 1 #134 - 2 msgs

Vibin R vinu at btc.iitb.ac.in
Sat Nov 23 12:16:43 CET 2002

> > 	While doing simulated annealing a considerable percentage of the
> > structures recovered after cooling is found to be having cis amides, with
> > omega angle close to zero value. Can I some artificial means increase the
> > value of the force constant, so that the planarity of the amide bond is
> > maintained even at higher temperatures. If yes, I guess i may have to make
> > changes in ffG43a1bon.itp file. But where exactly should i change and to
> > what extent is permissible. 

> Do you mean they go from trans to cis? At what temperature?

	Yes. It is. At 1000K
> You can indeed change the force field parameters in the ff*bon.itp
> files. 

Can I increase dihedral angle potential value (33.5) twice or ten times
in the following dihedral angle definition in ffG43a1bon.itp file

#define gd_4    180.000       33.5          2
; -C-N, NT, NE, NZ,NR-  8.0


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