AMBER: les/nudged elastic band

From: Tamara Rogers <>
Date: Thu, 31 May 2007 16:20:21 -0700 (PDT)

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?

Luggage? GPS? Comic books?
Check out fitting gifts for grads at Yahoo! Search.
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Jun 03 2007 - 06:07:29 PDT
Custom Search