Validation of MHPC512: A Publicly Available Special-Purpose Supercomputer for Molecular Dynamics Simulations of Biomolecular Systems

Abstract

MHPC512 is a massively parallel, special-purpose supercomputer designed primarily for atomic-level molecular dynamics (MD) simulations of biomolecular systems. It comprises 512 processor units interconnected by a high-speed three-dimensional torus network and employs a custom chip architecture that uses 35-bit fixed-point arithmetic to accelerate computation while controlling precision loss within an acceptable margin. The preprocessor is compatible with GROMACS and AMBER input formats and supports widely used biomolecular force fields (including CHARMM, AMBER, and OPLS/AA), the Neutral Territory method for short-range nonbonded interactions, the k-space Gaussian Split Ewald method for long-range electrostatics, and multiple thermostats, barostats, and integrators. We present a three-tier validation protocol--comparing static energy and virial components, examining ensemble distributions (NVE, NVT, NPT), and evaluating long-time statistical properties--demonstrating that MHPC512 reproduces results consistent with GROMACS and AmberTools. Application examples, including bulk water, dipeptide conformational sampling, folding of fast-folding peptides, membrane-protein systems, lipid self-assembly, and GPCR conformational transitions, further confirm its reliability. MHPC512 has been deployed at multiple supercomputing centers and is publicly accessible, representing a significant advance in high-throughput, large-scale biomolecular MD simulations.