CD and MD - Molecular Dynamics

Posted by Anthony Nicholls on Nov 26, 2013 1:29:24 PM

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.

Anthony

Download the slides.

Preserved Comment

Ant,
  • Agree that solving approximate model exactly is not optimal - but solving an approximate model carelessly is worthless (think about all the PhII drop-out where we don't know whether it is mechanism or target engagement) at least try to figure out why your understanding (belief?) failed
  • Woody should have said "Energy function and Sampling" - b/c that is correct. Schrodinger (the real Scientist) is right enough for our atomic systems & I don't see any thing in Stat Mech that concerns me (yes - fuck the ergodicity argument - you will lose on that one)
  • where was the ack on FreeForm today to Gilson (who is in the WvG no BS class)
  • the ToT on the OE web-site is spectacular - you guys have totally nailed it !!

Congrats ! 

Brock

Topic: Ant's Rants