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

JOURNAL OF MOLECULAR BIOLOGY

卷:433

Article

Jewett, Andrew, I¹  Stelter, David²  Lambert, Jason³  Saladi, Shyam M.⁴  Roscioni, Otello M.⁵  Ricci, Matteo⁵  Autin, Ludovic¹  Maritan, Martina¹  Bashusqeh, Saeed M.⁶  Keyes, Tom²  Dame, Remus T.⁷  Shea, Joan-Emma^8,9  Jensen, Grant J.^4,10  Goodsell, David S.^1,11,12 

[1] Scripps Res Inst, Dept Integrat Struct & Computat Biol, La Jolla, CA 92037 USA

[2] Boston Univ, Dept Chem, Boston, MA 02215 USA

[3] Univ Tennessee, Dept Chem, Knoxville, TN 37996 USA

[4] CALTECH, Div Biol & Biol Engn, Pasadena, CA 91125 USA

[5] MaterialX LTD, Bristol, Avon, England

[6] Univ Tehran, Coll Engn, Sch Mech Engn, Tehran, Iran

[7] Leiden Univ, Leiden Inst Chem, Leiden, Netherlands

[8] Univ Calif Santa Barbara, Dept Chem & Biochem, Santa Barbara, CA 93106 USA

[9] Univ Calif Santa Barbara, Dept Phys, Santa Barbara, CA 93106 USA

[10] CALTECH, Howard Hughes Med Inst, Pasadena, CA 91125 USA

[11] Rutgers State Univ, RCSB Prot Data Bank, Piscataway, NJ USA

[12] Rutgers State Univ, Inst Quantitat Biomed, Piscataway, NJ USA

关键词: coarse-grained simulation;    molecular modeling;    LAMMPS;    molecular dynamics;   

DOI  :  10.1016/j.jmb.2021.166841

来源: Elsevier

【 摘 要 】

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. (C) 2021 Elsevier Ltd. All rights reserved.

【 授权许可】

Free