Campuses:

Milestoning, Extending Time Scale of Molecular Simulations

Thursday, July 26, 2007 - 9:15am - 9:55am
EE/CS 3-180
Ron Elber (The University of Texas at Austin)
A new computational algorithm to extend time
scales of
atomically detailed simulations is illustrated. The
algorithm
(Milestoning) is based on partitioning the dynamics to a
sequence of
trajectories between “milestones” and constructing a
non-Markovian
model for the motion along a reaction coordinate.
Besides toy models, two molecular systems are discussed:
(i) The
kinetics of a conformational transition in a blocked
alanine is computed
and shown to be accurate, more efficient than
straightforward Molecular
Dynamics by a factor of about 9, and non-exponential. (ii)
The allosteric
conformational transition in Scapharca hemoglobin is
calculated. The
results for the rate (about 10+/-9 microseconds) are in
accord with
experiment and are obtained about 1,000 times faster than
straightforward
Molecular Dynamics. No assumption of an activated process
or states
separated by significant barrier is made.
A general scaling argument predicts linear speed-up with
the number of
milestones for diffusive processes, and exponential
speed-up for
transitions over barriers. The algorithm is also trivial to
parallelize.
As a side result Milestoning also produces the free energy
profile along
the reaction coordinate, and is able to describe
non-equilibrium motions
along one (or a few) degrees of freedom.