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

[David]

On Sat, 2002-11-23 at 11:49, Vibin R wrote:
> > > 	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
Yes, but you will get higher frequency motions, and hence have to reduce
your timestep.

> 
> Thanks
> vibin
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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