Jejoong Yoo | Searcharxiv

arXiv2023

GPU acceleration of many-body perturbation theory methods in MOLGW with OpenACC

Quasiparticle self-consistent many-body perturbation theory (MBPT) methods that update both eigenvalues and eigenvectors can calculate the excited-state properties of molecular systems without depending on the choice of starting points. However, those methods are computationally intensive even on modern multi-core central processing units (CPUs) and thus typically limited to small systems. Many-core accelerators such as graphics processing units (GPUs) may be able to boost the performance of those methods without losing accuracy, making starting-point-independent MBPT methods applicable to large systems. Here, we GPU accelerate MOLGW, a Gaussian-based MBPT code for molecules, with open accelerators (OpenACC) and achieve speedups of up to 9.7x over 32 open multi-processing (OpenMP) CPU threads.

cond-mat.mtrl-sci↗

arXiv2015

Improved Parameterization of Amine-Carboxyate and Amine-Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields

Over the past decades, molecular dynamics (MD) simulations of biomolecules have become a mainstream biophysics technique. As the length and time scales amenable to the MD method increase, shortcomings of the empirical force fields---which have been developed and validated using relatively short simulations of small molecules---become apparent. One common artifact is aggregation of water-soluble biomolecules driven by artificially strong charge--charge interactions. Here, we report a systematic refinement of Lennard-Jones parameters (NBFIX) describing amine--carboxylate and amine--phosphate interactions, which brings MD simulations of basic peptide-mediated nucleic acids assemblies and lipid bilayer membranes in better agreement with experiment. As our refinement neither affects the existing parameterization of bonded interaction nor does it alter the solvation free energies, it improves realism of an MD simulation without introducing additional artifacts.

physics.bio-ph↗