CD and MD

By | November 26, 2013

When the recent Nobel Prize for Chemistry was announced, going to Karplus, Levitt and Warshel I assumed it must have been for “Services to Molecular Dynamics”. As such, I joined the debate on Derek Lowe’s “In The Pipeline” on whether the field had earned such recognition:

It turned out, of course, that the Swedes had QM/MM in mind, not MD, but by the time I, and others, realized this positions were staked out! As a consequence, Ashutosh Jogalekar, who has his own blog, “Curious Wavefunction”, and who works in Boston at Ensemble Therapeutics, asked me if I would give a more detailed exposition of my concerns at one of the OpenEye lunchtime seminars. This I duly did on October the 30th. For those of you who could not attend but are interested, I am posting an annotated version of that PowerPoint presentation. I realize that many people like MD and that a good number of my friends and colleagues believe it can be made more predictive. However, as a technique MD has many attractive attributes that have nothing to do with its actual predictive capabilities (it makes great movies, it’s “Physics”, calculations take a long time, it takes skill to do right, “important” people develop it, etc). As I repeatedly mentioned in the talk, I would love MD to be a reliable tool – many of the things modelers try to do would become much easier. I just see little objective, scientific evidence for this as yet. In particular, it bothers me that MD is not held to the same standards of proof that many simpler, empirical approaches are – and this can’t be good for the field or MD.


Download the slides.


Anthony Nicholls

CEO & Founder of OpenEye Scientific Software, Inc.

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