[gmx-users] Support of Saddle Point Calculations

David van der Spoel spoel at xray.bmc.uu.se
Sun Oct 19 22:14:32 CEST 2008

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
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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

More information about the gromacs.org_gmx-users mailing list