Table 1.

Computational throughput (ps/day) of QM/MM TeraChem/AMBER molecular dynamics of PYP using a 0.5fs time step. File and MPI based communication are compared for QM regions 1 (R1) and 3 (R3) over 1, 2, and 4 GPUs (Tesla C2050 GPU cards). The QM region is modeled with the B3LYP/6-31G method. Calculations were performed on a dual Intel Xeon X5570 workstation with 72 GB RAM. Results are presented for both generating an initial wave function guess from atomic densities and for using the wave function from the previous time step as an initial guess in the SCF process.

	QM R1 (139 basis fxns)			QM R3 (541 basis fxns)
# of GPUs	1	2	4	1	2	4
File, guess generated	2.75	2.80	2.40	0.48	0.76	0.96
MPI, guess generated	3.63	4.49	4.63	0.50	0.85	1.25
File, reuse guess	3.44	3.20	2.11	0.75	1.11	1.24
MPI, reuse guess	4.82	5.61	5.82	0.80	1.33	1.90
MPI, guess read, no MM	5.00	5.99	6.34	0.84	1.39	2.01