[gmx-users] cation-pi interaction
chris.neale at mail.utoronto.ca
Sun Jun 2 18:55:31 CEST 2013
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?
-- 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.
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