A clear description of minimum free energy pathways (MFEP) provides insight into statistical and dynamical properties of biomolecules. Applicability of traditional molecular dynamics (MD) can be limited in locating MFEP’s of complex systems with rugged multidimensional free energy landscapes. Partial nudged elastic band (PNEB) in combination with simulated annealing has proven successful in identifying such dominant pathways. In NEB, a series of consecutively connected replicas, form a discrete pathway with tunable resolution. Harmonic springs couple the dynamics of adjacent systems and the generated ensemble evolves into a smooth transition path.<br/>We provide a CUDA enabled implementation of PNEB, that operates on the pmemd module of AMBER. Meticulous optimizations in data transfer between the message passing interface (MPI) ranks along with porting the code to graphics processing units (GPUs) resulted in more than two orders of magnitude speedup on a Tesla P100 GPU in comparison to two Intel Xeon Platinum 8160 processors, while numerical accuracy is uncompromised. The new fast and accurate multi-GPU implementation of PNEB in AMBER molecular dynamics software suite can contribute to the design of novel drug materials without the need to access massive computational resources.

Implementation of GPU-accelerated partial nudged elastic band method in AMBER

2019 Spring National Meeting

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