AMBER Archive (2007)

Subject: RE: AMBER: les/nudged elastic band

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu May 31 2007 - 18:59:25 CDT

Hi Tamara,
 
The thing to remember when running QM/MM simulations is that the actual
bonding information in the prmtop file is not used for the QM region. Hence
while the two end points have to have identical topology files this in no
way prevents you breaking a bond along the reaction coordinate in NEB
assuming that that bond is within the QM region. You will see no difference
in the results if you don't have the bond in both end states or do have the
bond specified in both end states - the choice is yours.
 
All the best
Ross

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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Tamara Rogers
Sent: Thursday, May 31, 2007 16:20
To: amber_at_scripps.edu
Subject: AMBER: les/nudged elastic band

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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