ArticleJournal of molecular biology2021
Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics.
Article in Journal of molecular biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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92 citing papers in PubMed.
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- Reconciling strong coordination and anion-reinforced solvation structure enables nonflammable electrolytes for potassium-ion batteries.Nature communications · 2026Article
- Conformational Isomerization of Imide Anions Governs Solvation and Transport in Water-in-Salt Electrolytes.Journal of the American Chemical Society · 2026Article
- MolPy: A Large Language Model-Friendly Toolkit for Reactive Topology Editing in Polymer Simulations.Journal of chemical information and modeling · 2026Article
- Collective fluctuations underlying nanobody inhibitory activity targetingbioRxiv : the preprint server for biology · 2026Article
- Bioinspired Nanofluidic Memristors Based on Polyelectrolyte Conformation for Synaptic Learning and in-Memory Logic Computing.Advanced materials (Deerfield Beach, Fla.) · 2026Article
- Water-Network-Triggered Breakdown: Multiscale Theoretical Insights into PET Hydrolysis under Working Conditions.The journal of physical chemistry. B · 2026Article
- CASPULE: A computational tool to study sticker spacer polymer condensates.PLoS computational biology · 2026Article
- Effect of Plasticizers on Performance in Single-Ion Conducting Polymer Electrolytes: Implications for Lithium-Ion Batteries.Energy & fuels : an American Chemical Society journal · 2026Article
- Cation design in complex aqueous electrolytes for low-temperature zinc-bromine flow batteries.Nature communications · 2026Article
- Effects of van der Waals Interaction on NACS omega · 2026Article
- Mechanistic insights into lenacapavir-induced off-pathway HIV-1 capsid assembly.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Article
- A Coarse-Grained MARTINI Model for Mucins.Journal of chemical theory and computation · 2026Article
- Biomimetic action-potential transmission via mechano-gated potassium channels assembled by quadruple hydrogen-bonded crown ethers.Science advances · 2026Article
- Electrically Tunable Friction through Surface Adsorption Layer Restructuring.ACS applied materials & interfaces · 2025Article
- Gene loci fluctuations reveal bacterial chromosome dynamical organization.Communications biology · 2025Article
- Atomistic Polymer Modeling: Recent Advances and Challenges in Building and Parametrization Workflows.Macromolecules · 2025Review
32 more citing papers are in PubMed but not listed here.
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14 authors.
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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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.