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Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics

Jewett, Andrew I. and Stelter, David and Lambert, Jason and Saladi, Shyam M. and Roscioni, Otello M. and Ricci, Matteo and Autin, Ludovic and Maritan, Martina and Bashusqeh, Saeed M. and Keyes, Tom and Dame, Remus T. and Shea, Joan-Emma and Jensen, Grant J. and Goodsell, David S. (2021) Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics. Journal of Molecular Biology, 433 (11). Art. No. 166841. ISSN 0022-2836. doi:10.1016/j.jmb.2021.166841. https://resolver.caltech.edu/CaltechAUTHORS:20210210-100826621

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Abstract

Coarse-grained models have long been considered indispensable tools in the investigation of biomolecular dynamics and assembly. However, the process of simulating such models is arduous because unconventional force fields and particle attributes are often needed, and some systems are not in thermal equilibrium. Although modern molecular dynamics programs are highly adaptable, software designed for preparing all-atom simulations typically makes restrictive assumptions about the nature of the particles and the forces acting on them. Consequently, the use of coarse-grained models has remained challenging. Moltemplate is a file format for storing coarse-grained molecular models and the forces that act on them, as well as a program that converts moltemplate files into input files for LAMMPS, a popular molecular dynamics engine. Moltemplate has broad scope and an emphasis on generality. It accommodates new kinds of forces as they are developed for LAMMPS, making moltemplate a popular tool with thousands of users in computational chemistry, materials science, and structural biology. To demonstrate its wide functionality, we provide examples of using moltemplate to prepare simulations of fluids using many-body forces, coarse-grained organic semiconductors, and the motor-driven supercoiling and condensation of an entire bacterial chromosome.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1016/j.jmb.2021.166841DOIArticle
http://moltemplate.orgRelated ItemMoltemplate
ORCID:
AuthorORCID
Jewett, Andrew I.0000-0002-6252-9888
Stelter, David0000-0001-8493-5118
Lambert, Jason0000-0003-0608-4332
Saladi, Shyam M.0000-0001-9701-3059
Roscioni, Otello M.0000-0001-7815-6636
Ricci, Matteo0000-0002-4534-6318
Autin, Ludovic0000-0002-2197-191X
Maritan, Martina0000-0001-9901-1153
Dame, Remus T.0000-0001-9863-1692
Shea, Joan-Emma0000-0002-9801-9273
Jensen, Grant J.0000-0003-1556-4864
Goodsell, David S.0000-0002-5932-2130
Additional Information:© 2021 Elsevier Ltd. Received 22 September 2020, Revised 19 January 2021, Accepted 20 January 2021, Available online 2 February 2021. Moltemplate was supported by NIH grants T32-AI007354-29, GM120604 and GM122588, NSF-MCB-1158577 and NSF-MCB-1716956, and HFSP RGP0014/2014. We thank Valeria Molinero, Yandong Zhang, Nathaniel Charest, William M. Clemons Jr., David Keffer, Marcus Martin, Paul Saxe and Robert Compton for support and useful discussions. Code availability: Moltemplate (available at http://moltemplate.org) is free open-source software. It is distributed under the MIT and PSF licenses. Moltemplate uses modern tools for public collaborative development and has many contributors. Users contribute suggestions, bug-reports, code, force-fields, examples, and documentation using GitHub. TravisCI is used for continuous-integration. Author contributions: AJ conceived, developed the original software, and carried out simulations. DS, JL, SMS, and OMR, contributed code improvements. OMR and MR contributed the MOLC example. SMB contributed the MARTINI example. MM, LA, and DSG created the mycoplasma models. AJ and DSG drafted the manuscript. DSG, GJJ, JES, TK, and RTD, planned and supervised the work. CRediT authorship contribution statement: Andrew I. Jewett: Conceptualization, Software, Investigation, Writing - original draft, Writing - review & editing. David Stelter: Investigation, Software, Writing - review & editing. Jason Lambert: Software, Writing - review & editing. Shyam M. Saladi: Software, Writing - review & editing. Otello M. Roscioni: Software, Investigation, Writing - review & editing. Matteo Ricci: Investigation, Writing - review & editing. Ludovic Autin: Investigation, Writing - review & editing. Martina Saeed M. Maritan Bashusqeh: Investigation, Writing - review & editing, Investigation, Writing - review & editing. Tom Keyes: Supervision, Writing - review & editing. Remus T. Dame: Supervision, Writing - review & editing. Joan-Emma Shea: Supervision, Writing - review & editing. Grant J. Jensen: Supervision, Writing - review & editing. David S. Goodsell: Supervision, Writing - original draft, Writing - review & editing. The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Funders:
Funding AgencyGrant Number
NIH Predoctoral FellowshipT32-AI007354-29
NIHGM120604
NIHGM122588
NSFMCB-1158577
NSFMCB-1716956
Human Frontier Science ProgramRGP0014/2014
Subject Keywords:coarse-grained simulation, molecular modeling, LAMMPS, molecular dynamics
Issue or Number:11
DOI:10.1016/j.jmb.2021.166841
Record Number:CaltechAUTHORS:20210210-100826621
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210210-100826621
Official Citation:Andrew I. Jewett, David Stelter, Jason Lambert, Shyam M. Saladi, Otello M. Roscioni, Matteo Ricci, Ludovic Autin, Martina Maritan, Saeed M. Bashusqeh, Tom Keyes, Remus T. Dame, Joan-Emma Shea, Grant J. Jensen, David S. Goodsell, Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics, Journal of Molecular Biology, Volume 433, Issue 11, 2021, 166841, ISSN 0022-2836, https://doi.org/10.1016/j.jmb.2021.166841. (https://www.sciencedirect.com/science/article/pii/S0022283621000358)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:107983
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:10 Feb 2021 18:25
Last Modified:12 May 2021 16:30

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