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Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations

Residue-level coarse-grained (CG) models have become one of the most popular tools in biomolecular simulations in the trade-off between modeling accuracy and computational efficiency. To investigate large-scale biological phenomena in molecular dynamics (MD) simulations with CG models, unified treat...

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Autores principales: Tan, Cheng, Jung, Jaewoon, Kobayashi, Chigusa, Torre, Diego Ugarte La, Takada, Shoji, Sugita, Yuji
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9012402/
https://www.ncbi.nlm.nih.gov/pubmed/35381009
http://dx.doi.org/10.1371/journal.pcbi.1009578
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author Tan, Cheng
Jung, Jaewoon
Kobayashi, Chigusa
Torre, Diego Ugarte La
Takada, Shoji
Sugita, Yuji
author_facet Tan, Cheng
Jung, Jaewoon
Kobayashi, Chigusa
Torre, Diego Ugarte La
Takada, Shoji
Sugita, Yuji
author_sort Tan, Cheng
collection PubMed
description Residue-level coarse-grained (CG) models have become one of the most popular tools in biomolecular simulations in the trade-off between modeling accuracy and computational efficiency. To investigate large-scale biological phenomena in molecular dynamics (MD) simulations with CG models, unified treatments of proteins and nucleic acids, as well as efficient parallel computations, are indispensable. In the GENESIS MD software, we implement several residue-level CG models, covering structure-based and context-based potentials for both well-folded biomolecules and intrinsically disordered regions. An amino acid residue in protein is represented as a single CG particle centered at the Cα atom position, while a nucleotide in RNA or DNA is modeled with three beads. Then, a single CG particle represents around ten heavy atoms in both proteins and nucleic acids. The input data in CG MD simulations are treated as GROMACS-style input files generated from a newly developed toolbox, GENESIS-CG-tool. To optimize the performance in CG MD simulations, we utilize multiple neighbor lists, each of which is attached to a different nonbonded interaction potential in the cell-linked list method. We found that random number generations for Gaussian distributions in the Langevin thermostat are one of the bottlenecks in CG MD simulations. Therefore, we parallelize the computations with message-passing-interface (MPI) to improve the performance on PC clusters or supercomputers. We simulate Herpes simplex virus (HSV) type 2 B-capsid and chromatin models containing more than 1,000 nucleosomes in GENESIS as examples of large-scale biomolecular simulations with residue-level CG models. This framework extends accessible spatial and temporal scales by multi-scale simulations to study biologically relevant phenomena, such as genome-scale chromatin folding or phase-separated membrane-less condensations.
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spelling pubmed-90124022022-04-16 Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations Tan, Cheng Jung, Jaewoon Kobayashi, Chigusa Torre, Diego Ugarte La Takada, Shoji Sugita, Yuji PLoS Comput Biol Research Article Residue-level coarse-grained (CG) models have become one of the most popular tools in biomolecular simulations in the trade-off between modeling accuracy and computational efficiency. To investigate large-scale biological phenomena in molecular dynamics (MD) simulations with CG models, unified treatments of proteins and nucleic acids, as well as efficient parallel computations, are indispensable. In the GENESIS MD software, we implement several residue-level CG models, covering structure-based and context-based potentials for both well-folded biomolecules and intrinsically disordered regions. An amino acid residue in protein is represented as a single CG particle centered at the Cα atom position, while a nucleotide in RNA or DNA is modeled with three beads. Then, a single CG particle represents around ten heavy atoms in both proteins and nucleic acids. The input data in CG MD simulations are treated as GROMACS-style input files generated from a newly developed toolbox, GENESIS-CG-tool. To optimize the performance in CG MD simulations, we utilize multiple neighbor lists, each of which is attached to a different nonbonded interaction potential in the cell-linked list method. We found that random number generations for Gaussian distributions in the Langevin thermostat are one of the bottlenecks in CG MD simulations. Therefore, we parallelize the computations with message-passing-interface (MPI) to improve the performance on PC clusters or supercomputers. We simulate Herpes simplex virus (HSV) type 2 B-capsid and chromatin models containing more than 1,000 nucleosomes in GENESIS as examples of large-scale biomolecular simulations with residue-level CG models. This framework extends accessible spatial and temporal scales by multi-scale simulations to study biologically relevant phenomena, such as genome-scale chromatin folding or phase-separated membrane-less condensations. Public Library of Science 2022-04-05 /pmc/articles/PMC9012402/ /pubmed/35381009 http://dx.doi.org/10.1371/journal.pcbi.1009578 Text en © 2022 Tan et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Tan, Cheng
Jung, Jaewoon
Kobayashi, Chigusa
Torre, Diego Ugarte La
Takada, Shoji
Sugita, Yuji
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations
title Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations
title_full Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations
title_fullStr Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations
title_full_unstemmed Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations
title_short Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations
title_sort implementation of residue-level coarse-grained models in genesis for large-scale molecular dynamics simulations
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9012402/
https://www.ncbi.nlm.nih.gov/pubmed/35381009
http://dx.doi.org/10.1371/journal.pcbi.1009578
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