Re: [gmx-users] cation-pi interaction

2013-06-02 Thread Mark Abraham
Chapter 8 of the manual names a tool that sounds like what the OP wants ;-) Mark On Sat, Jun 1, 2013 at 10:25 AM, Dr. Vitaly Chaban wrote: > Can g_angle not handle this? > > > Dr. Vitaly Chaban > > > > > > On Sat, Jun 1, 2013 at 10:15 AM, larif sofiene >wrote: > > > Greeting > > I'm trying to

[gmx-users] cation-pi interaction

2013-06-02 Thread 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

Re: [gmx-users] cation-pi interaction

2013-06-01 Thread Dr. Vitaly Chaban
Can g_angle not handle this? Dr. Vitaly Chaban On Sat, Jun 1, 2013 at 10:15 AM, larif sofiene wrote: > Greeting > 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 angl

[gmx-users] cation-pi interaction

2013-06-01 Thread larif sofiene
Greeting 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). H