Thank you David, I am about halfway through the Gromacs 2007 Workshop material. Very nice. I'm wondering if there is any workshop videos covering QM/MM methods in Gromacs.
Thanks, Jack On Sun, Oct 19, 2008 at 4:14 PM, David van der Spoel <[EMAIL PROTECTED]>wrote: > 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@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 [EMAIL PROTECTED] >> 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. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
_______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php