[gmx-users] Transition State Optimization Algorithms in GROMACS

[Gerrit Groenhof]

> 
> On Thu, 2004-08-26 at 07:55, Dr Seth Carlton OLSEN wrote:
> > Dear Collegues,
> > 
> > Is there a transition state optimization algorithm available for use with the GROMACS package?  If so, are there examples of its use in the literature?  
> > 
> I'm not aware of anything. Gromacs does not know anything about
> reactions, however, you could probably do a minimization with
> restraints.

Indeed, if you can define your reaction coordinate in terms of bonds
you can simply constrain thatdegree of freedom, while minimizing all
the others. I am creating a web tutorial on QM/MM with gromacs
demonstrating how to use such so-called linear transit to calculate
reaction pathways and locate transition states. But of course it will
work without QM as well.

Good luck,

Gerrit


> 
> Maybe you can extend a bit on what you're trying to do.
> > Cheers,
> > 
> > Seth Olsen
> > 
> > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
> > 
> > Dr Seth Olsen, PhD
> > Postdoctoral Fellow, Computational Systems Biology Group
> > Centre for Computational Molecular Science
> > Chemistry Building,
> > The University of Queensland
> > Qld 4072, Brisbane, Australia
> > 
> > tel (617) 33653732
> > fax (617) 33654623
> > email: s.olsen1 at uq.edu.au
> > Web: www.ccms.uq.edu.au
> > 
> > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
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> > 
> > 
> > 
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> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
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