Review of Electrostatic Force Calculation Methods and Their Acceleration in Molecular Dynamics Packages Using Graphics Processors

Overview

Journal ACS Omega

Publisher American Chemical Society

Specialty Chemistry

Date 2022 Sep 26

PMID 36157750

Authors

Anu George

Sandip Mondal

Madhura Purnaprajna

Prashanth Athri

Affiliations

Soon will be listed here.

Abstract

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 (, 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.

Citing Articles

Phytochemical Analysis, Computational Study, and in vitro Assay of Inflorescence Extract Towards Inducible Nitric Oxide Synthase.

Prayoga D, Pitaloka D, Aulifa D, Budiman A, Levita J, Jiranusornkul S J Exp Pharmacol. 2025; 17:123-141.

PMID: 40078169 PMC: 11899951. DOI: 10.2147/JEP.S505658.

Elucidating the binding specificity of interactive compounds targeting ATP-binding cassette subfamily G member 2 (ABCG2).

Kumar P, Kumari I, Prasad R, Ray S, Banerjee A, Prakash A Mol Divers. 2025; .

PMID: 39786520 DOI: 10.1007/s11030-024-11078-2.

Embracing exascale computing in nucleic acid simulations.

Li J, Zhou Y, Chen S Curr Opin Struct Biol. 2024; 87:102847.

PMID: 38815519 PMC: 11283969. DOI: 10.1016/j.sbi.2024.102847.

References

Andoh Y, Yoshii N, Fujimoto K, Mizutani K, Kojima H, Yamada A . MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program for Large-Scale Systems with Long-Range Forces Calculated by Fast Multipole Method (FMM) and Highly Scalable Fine-Grained New Parallel Processing Algorithms. J Chem Theory Comput. 2015; 9(7):3201-9. DOI: 10.1021/ct400203a. View

Shaw D . A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. J Comput Chem. 2005; 26(13):1318-28. DOI: 10.1002/jcc.20267. View

Reif M, Krautler V, Kastenholz M, Daura X, Hunenberger P . Molecular dynamics simulations of a reversibly folding beta-heptapeptide in methanol: influence of the treatment of long-range electrostatic interactions. J Phys Chem B. 2009; 113(10):3112-28. DOI: 10.1021/jp807421a. View

Phillips J, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E . Scalable molecular dynamics with NAMD. J Comput Chem. 2005; 26(16):1781-802. PMC: 2486339. DOI: 10.1002/jcc.20289. View

Neelov A, Holm C . Interlaced P3M algorithm with analytical and ik-differentiation. J Chem Phys. 2010; 132(23):234103. DOI: 10.1063/1.3430521. View

Field M . Technical advances in molecular simulation since the 1980s. Arch Biochem Biophys. 2015; 582:3-9. DOI: 10.1016/j.abb.2015.03.005. View

Moore S, Crozier P . Extension and evaluation of the multilevel summation method for fast long-range electrostatics calculations. J Chem Phys. 2014; 140(23):234112. DOI: 10.1063/1.4883695. View

Pall S, Zhmurov A, Bauer P, Abraham M, Lundborg M, Gray A . Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS. J Chem Phys. 2020; 153(13):134110. DOI: 10.1063/5.0018516. View

Piana S, Lindorff-Larsen K, Dirks R, Salmon J, Dror R, Shaw D . Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations. PLoS One. 2012; 7(6):e39918. PMC: 3386949. DOI: 10.1371/journal.pone.0039918. View

10.

Reumann M, Fitch B, Rayshubskiy A, Pitman M, Rice J . Orthogonal recursive bisection as data decomposition strategy for massively parallel cardiac simulations. Biomed Tech (Berl). 2011; 56(3):129-45. DOI: 10.1515/BMT.2011.100. View

11.

Selvaraj J, Sundar P S, Rajan L, Selvaraj D, Palanisamy D, Namboori Pk K . Identification of (2,3)-2-(3,4-dihydroxyphenyl)chroman-3-yl-3,4,5-trihydroxy benzoate as multiple inhibitors of SARS-CoV-2 targets; a systematic molecular modelling approach. RSC Adv. 2022; 11(22):13051-13060. PMC: 8697517. DOI: 10.1039/d1ra01603b. View

12.

Kutzner C, van der Spoel D, Fechner M, Lindahl E, Schmitt U, de Groot B . Speeding up parallel GROMACS on high-latency networks. J Comput Chem. 2007; 28(12):2075-84. DOI: 10.1002/jcc.20703. View

13.

Gruber C, Pleiss J . Systematic benchmarking of large molecular dynamics simulations employing GROMACS on massive multiprocessing facilities. J Comput Chem. 2010; 32(4):600-6. DOI: 10.1002/jcc.21645. View

14.

Patel C, Goswami D, Jaiswal D, Parmar R, Solanki H, Pandya H . Pinpointing the potential hits for hindering interaction of SARS-CoV-2 S-protein with ACE2 from the pool of antiviral phytochemicals utilizing molecular docking and molecular dynamics (MD) simulations. J Mol Graph Model. 2021; 105:107874. PMC: 7897937. DOI: 10.1016/j.jmgm.2021.107874. View

15.

Padhi A, Rath S, Tripathi T . Accelerating COVID-19 Research Using Molecular Dynamics Simulation. J Phys Chem B. 2021; 125(32):9078-9091. DOI: 10.1021/acs.jpcb.1c04556. View

16.

Hess B, Kutzner C, van der Spoel D, Lindahl E . GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J Chem Theory Comput. 2015; 4(3):435-47. DOI: 10.1021/ct700301q. View

17.

Wang J, Wolf R, Caldwell J, Kollman P, Case D . Development and testing of a general amber force field. J Comput Chem. 2004; 25(9):1157-74. DOI: 10.1002/jcc.20035. View

18.

Patra M, Karttunen M, Hyvonen M, Falck E, Lindqvist P, Vattulainen I . Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions. Biophys J. 2003; 84(6):3636-45. PMC: 1302948. DOI: 10.1016/S0006-3495(03)75094-2. View

19.

Alazmi M, Motwalli O . virtual screening, characterization, docking and molecular dynamics studies of crucial SARS-CoV-2 proteins. J Biomol Struct Dyn. 2020; 39(17):6761-6771. PMC: 7484580. DOI: 10.1080/07391102.2020.1803965. View

20.

Cruz F, de Pablo J, Mota J . Endohedral confinement of a DNA dodecamer onto pristine carbon nanotubes and the stability of the canonical B form. J Chem Phys. 2014; 140(22):225103. DOI: 10.1063/1.4881422. View