Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born.

Journal of Chemical Theory and Computation
Andreas W GötzRoss C Walker

Abstract

We present an implementation of generalized Born implicit solvent all-atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA enabled NVIDIA graphics processing units (GPUs). We discuss the algorithms that are used to exploit the processing power of the GPUs and show the performance that can be achieved in comparison to simulations on conventional CPU clusters. The implementation supports three different precision models in which the contributions to the forces are calculated in single precision floating point arithmetic but accumulated in double precision (SPDP), or everything is computed in single precision (SPSP) or double precision (DPDP). In addition to performance, we have focused on understanding the implications of the different precision models on the outcome of implicit solvent MD simulations. We show results for a range of tests including the accuracy of single point force evaluations and energy conservation as well as structural properties pertainining to protein dynamics. The numerical noise due to rounding errors within the SPSP precision model is sufficiently large to lead to an accumulation of errors which can result in unphysical trajectories for long time scale simula...Continue Reading

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Methods Mentioned

BETA
NMR

Software Mentioned

Intel
OpenMM
AMBER
OpenGL
allGather
CURAND
GPUDirect
RedHat Enterprise Linux
AmberTools
OpenCL

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