AMBER Archive (2009)

Subject: [AMBER] analysis of QM/MM - LCOD

From: Aust, Susanne (
Date: Fri Jul 03 2009 - 04:51:34 CDT

Dear all,
i calculated with Amber10 a QM/MM MD simulation with the special LCOD method
(2 reactioncoordinates in the same calculation)
It works and I see more then the intiated cyclisation and proton separation.
Now my problem is, how can I analyse the results reasonable? I plot the
txtfile with the work (energy) vs. time)
But should I also analyse the energy over the whole QM - part?
Do you know a tutorial or literature?
Thanks for your help!
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