[AMBER] defining reaction coordinate for umbrella sampling

From: Jorgen Simonsen <jorgen589.gmail.com>
Date: Sun, 1 Jun 2014 18:12:32 -0700

Hi ,

I am trying to perform a QM/MM reaction and would like to sampling along a
reaction coordinate using umbrella sampling.

My reaction is a SN2 attack where atom 10, an oxygen of hydroxide, is
attack a carbon atom number 12, which is bound to a leaving group with atom
14 another oxygen.

I have set the system up like this:

     i = (10,12,14)
     r = (1.0,-1.0)

       anchor_position = 3.0
       anchor_strength = 10.0

end variable

I do not understand where I would defined maximum distance for my reaction
also it is not clear to me how you specify the intervals being sampling
along the reaction coordinate e.g. I would like to sample with a step size
of 0.2 Å for this reaction coordinate but after 6 Å I do not want to apply
any force for the reaction coordinate. I am using amber12 - thanks for any
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Received on Sun Jun 01 2014 - 18:30:02 PDT
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