Mark Abraham wrote: > Christian Seifert wrote: >> On Friday 22 June 2007 10:59, Bert de Groot wrote: > >> The hessian is the second (numerical) derivative of the atoms in the >> three dimensions. In the future, I want to calculate the hessian of >> molecules next to proteins, so the "small droplet of explicit water" >> will not work here. I do not understand, why I need to calculate the >> second derivatives of the atoms of the whole system, if I just need it >> of a small molecule. > > Er, technically the second derivative of the energy of the whole system > with respect to the coordinates of the atoms, but I'm sure you know that > :-) You could certainly produce an algorithm to do this for just a > subset of atoms' coordinates, but so far I guess it hasn't been done > because people haven't perceived any value in it. So if you're convinced > it's a useful thing to do, you can either calculate the lot and extract > the ones you want, or rework the code. >
In addition, be aware that you should expect some negative eigenvalues in such a case as for the subsystem you're most likely not in a minimum anymore. As Mark and David already noted it's not immediately clear which physical interpretation would correspond to such an approach. Bert ______________________________________ Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 37077 Goettingen, Germany tel: +49-551-2012308, fax: +49-551-2012302 http://www.mpibpc.mpg.de/groups/de_groot _______________________________________________ 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
