Long Timestep Molecular Dynamics on the Graphical Processing Unit.
Molecular dynamics (MD) simulations now play a key role in many areas of theoretical chemistry, biology, physics, and materials science. In many cases, such calculations are significantly limited by the massive amount of computer time needed to perform calculations of interest. Herein, we present Long Timestep Molecular Dynamics (LTMD), a method to significantly speed MD simulations. In particular, we discuss new methods to calculate the needed terms in LTMD as well as issues germane to a GPU implementation. The resulting code, implemented in the OpenMM MD library, can achieve a significant 6-fold speed increase, leading to MD simulations on the order of 5 μs/day using implicit solvent models.
Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA, Department of Computer Science, Eckerd College, Saint Petersburg, FL 33712, USA, and Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
James C
JC
Sweet
Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA, Department of Computer Science, Eckerd College, Saint Petersburg, FL 33712, USA, and Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
Ronald J
RJ
Nowling
Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA, Department of Computer Science, Eckerd College, Saint Petersburg, FL 33712, USA, and Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
Trevor
T
Cickovski
Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA, Department of Computer Science, Eckerd College, Saint Petersburg, FL 33712, USA, and Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
Christopher R
CR
Sweet
Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA, Department of Computer Science, Eckerd College, Saint Petersburg, FL 33712, USA, and Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
Vijay S
VS
Pande
Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA, Department of Computer Science, Eckerd College, Saint Petersburg, FL 33712, USA, and Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
Jesús A
JA
Izaguirre