July 5, 2017

New GPU-accelerated pmemdGTI module offers over 2 orders of magnitude speedup in free energy calculations

New in the AMBER pipeline: GPU-accelerated Thermodynamic Integration free energy method for fast and accurate protein-ligand binding affinity prediction.

The Laboratory for Biomolecular Simulation Research at Rutgers University, in a collaboration with Merck & Co., Inc., have recently reported the eagerly-awaited implementation of the thermodynamic integration method on the pmemd module of the AMBER 16 package on GPUs (pmemdGTI). The pmemdGTI code delivers over two orders of magnitude of speed-up relative to a single CPU core for the calculation of ligand-protein binding affinities with no statistically significant numerical differences, and extends the range of GPU-accelerated capabilities of pmemd to free energy calculations using thermodynamic integration. The pmemdGTI module thus provides a powerful new tool for computational enzymology and drug discovery applications. The current version can be installed as a software patch to AMBER16, and is expected to be available in the next official AMBER release. Details on the implementation, performance benchmarks and results for protein-ligand binding free energies have been reported in the Journal of Chemical Theory and Computation (DOI: 10.1021/acs.jctc.7b00102).

Figure 1. Performance of pmemdGTI for L51a mutation in Factor Xa (DOI: 10.1021/acs.jctc.7b00102).

Figure 2. (A, top) Timing Benchmarks (ns/day) for pmemdGTI running on various Nvidia GPUs. TI results are the L51a to L51bt mutation in Factor Xa in explicit solvent (41,563 total atoms) in the NVT ensemble using a 1 fs time step and PME electrostatics with the whole ligand defined as the TI region. (B, bottom) Performance speed up of pmemd and pmemdGTI for GPU-accelerated MD and TI simulations, respectively for L51a in Factor Xa. Details have been reported in J. Chem. Theory Comput. (DOI: 10.1021/acs.jctc.7b00102).

November 10, 2016

Darrin York's Attendance At Solvay Conference In Brussels

The Solvay Conference is among the most famous conference in chemistry and physics, and has been attended by countless Nobel laureates since its beginnings in 1911. The famous photograph, shown below, was taken at the fifth Solvay Conference in 1927, and includes 17 Nobel laureates or future Nobel laureates, out of the 29 attendants.  It is hosted in Brussels, Belgium, and this year it was held from October 19th through the 22nd. Darrin York attended this conference to present a talk. A photo of this year's conference is shown on top.