Benchmark the AMOEBA force field as implemented in OpenMM.
Click "Documents" and download the instruction manual to get started.
This project contains the files needed to benchmark the AMOEBA force field as implemented in OpenMM and TINKER. The contents are:
1) OpenMM and TINKER input files for six water boxes of progressively increasing size (216 through 288,000 molecules) and DHFR in explicit water from the Joint AMBER-CHARMM benchmark.
2) Script for automatically running the benchmark across different methods (i.e. force field and run parameters), systems, and platforms.
3) Output data from running the benchmark on a high performance compute node (CPU: 2x Intel Xeon E5-2643 3.30GHz, GPU: NVidia GeForce GTX Titan Black).
4) Instruction manual.
The simulations are NVT (298.15 K), 1 and 2 fs time steps (2 fs time step uses MTS algorithm), PME electrostatics with real space cutoff 7.0 Angstrom, vdW cutoff 9.0 Angstrom. Simulation speed is given in ns/day.
Sep 19, 2014