Re: [AMBER] How to get the free energy landscape from a MD simulation?

From: <>
Date: Thu, 24 Mar 2011 11:27:48 -0400 (EDT)


> my case: I need to do a PMF for some reaction coordinate (nucleophilic
> attack) using QM/MM facility in Amber 10. I read through steered MD
> simulation but it sounds to me (from the comments I get from Amber
> users/developers) that SMD is a bit doggy and some people getting some
> trouble to publish work with SMD. Is there any EASY and reliable
> alternative
> in Amber 10 that I can apply to do a PMF for NU or PT reactions in
> enzyme???
> do you have any tutorial/example for the methode you explain below to
> Catherine that I can use??

what I suggested for Catherine will not work for a QM/MM run, since you
probably wont see the reaction happen in a free simulation. Therefore,
some kind of bias will be neccessary. I have no problem with steered MD
per se, but a rigorous analysis will require extensive sampling and some
non-equilibrium theory like Jarzynski's equation. If you prefer an
equilibrium run, you could do an umbrella sampling calculations. Check out
Amber Tut A10 for a steered MD example, not sure if there is one on
umbrella sampling...

Kind Regards,


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Thu Mar 24 2011 - 08:30:07 PDT
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