[gmx-users] Support of Saddle Point Calculations

[David van der Spoel]

Jack Shultz wrote:
> Hello,
> 
> I am fairly new to GROMACS but I have spent time running tutorials for 
> several other molecular dynamics applications. I would like to know if 
> the current framework for GROMACS has support for methods that calculate 
> saddle point energy in first-order reactions. If so, are there examples 
> I can read about?

First, GROMACS does not support reactions, unless you use the QM/MM 
methods in which case you have to look into e.g. Gaussian's way of doing 
a Transition State optimization.

Second, you can do normal mode analysis which would give you indirectly 
the needed information, if you have a conformation that you know is the 
transition state.
> 
> Jack
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se