[gmx-users] cation-pi interaction

[Christopher Neale]

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.