Dear Amber users,
I have a bond breaking reaction that I which to follow using the combination of QMMD and LES/nudged elastic band. I followed the online tutorial and have a general sense of how to to perform such a simulation. However, in the tutorial it states that LES requires the all snapshots have the same topology. Does anyone have any experience using this approach when there is a change of topology during the reaction (i.e. bond breaking/forming). I intend to model the region of the changing topology using QM. In particular, how would I perform a classic transition state search using QMMD in Amber 9?
Regards,
Tamara
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Received on Sun Jun 03 2007 - 06:07:29 PDT
