I've always wondered why people do this. There are no pi electrons in your force field so it seems to me that if you find a stable "cation-pi" interaction in your simulations then that just implies that a real cation-pi interaction is not necessary to stabilize this particular conformation. That is, unless one is just after pretty pictures. Am I missing something?
Chris. -- original message -- I'm trying to find the angle between a cation and a benzene cycle from a MD trajectory. I'm really confused is there a tool for such calculations ? because i must find angle using a plan passing by the center of the cycle and vector (from cation to the mass center of the benzene cycle). How can i do it please ?. thanks in advance. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
