Open AccessReview of Electrostatic Force Calculation Methods and Their Acceleration in Molecular Dynamics Packages Using Graphics Processors
Author(s) -
Anu George,
Sandip Mondal,
Madhura Purnaprajna,
Prashanth Athri
Publication year - 2022
Publication title -
acs omega
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.779
H-Index - 40
ISSN - 2470-1343
DOI - 10.1021/acsomega.2c03189
Subject(s) - microsecond , molecular dynamics , acceleration , computation , bottleneck , newtonian dynamics , femtosecond , electrostatics , dynamics (music) , range (aeronautics) , computational science , graphics , computer science , statistical physics , physics , computational chemistry , chemistry , materials science , classical mechanics , algorithm , computer graphics (images) , optics , laser , acoustics , composite material , embedded system
Molecular dynamics (MD) simulations probe the conformational repertoire of macromolecular systems using Newtonian dynamic equations. The time scales of MD simulations allow the exploration of biologically relevant phenomena and can elucidate spatial and temporal properties of the building blocks of life, such as deoxyribonucleic acid (DNA) and protein, across microsecond (μs) time scales using femtosecond (fs) time steps. A principal bottleneck toward extending MD calculations to larger time scales is the long-range electrostatic force measuring component of the naive nonbonded force computation algorithm, which scales with a complexity of ( N , number of atoms). In this review, we present various methods to determine electrostatic interactions in often-used open-source MD packages as well as the implementation details that facilitate acceleration of the electrostatic interaction calculation.