CaltechAUTHORS
Published May 28, 2021 | Version Supplemental Material
Journal Article Open

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

Creators

  • 1. ROR icon Scripps Research Institute
  • 2. ROR icon Boston University
  • 3. ROR icon University of Tennessee at Knoxville
  • 4. ROR icon California Institute of Technology
  • 5. ROR icon University of Tehran
  • 6. ROR icon Leiden University
  • 7. ROR icon University of California, Santa Barbara
  • 8. ROR icon Rutgers, The State University of New Jersey

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.

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.

Attached Files

Supplemental Material - 1-s2.0-S0022283621000358-mmc1.pdf

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1-s2.0-S0022283621000358-mmc1.pdf

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Additional details

Identifiers

Eprint ID
107983
DOI
10.1016/j.jmb.2021.166841
Resolver ID
CaltechAUTHORS:20210210-100826621

Related works

Describes
10.1016/j.jmb.2021.166841 (DOI)
http://moltemplate.org (URL)

Funding

NIH Predoctoral Fellowship
T32-AI007354-29
NIH
GM120604
NIH
GM122588
NSF
MCB-1158577
NSF
MCB-1716956
Human Frontier Science Program
RGP0014/2014

Dates

Created
2021-02-10
Created from EPrint's datestamp field
Updated
2021-05-12
Created from EPrint's last_modified field

Caltech Custom Metadata

Caltech groups
Division of Biology and Biological Engineering (BBE)