Hi,
> 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,
Thomas
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
