[gmx-users] Support of Saddle Point Calculations

[Jack Shultz]

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
<spoel at xray.bmc.uu.se>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 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
> _______________________________________________
> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081020/47e9d012/attachment.html>