ArticleJournal of chemical information and modeling2018
GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features.
Article in Journal of chemical information and modeling, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 224 papers.
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224 citing papers in PubMed.
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- Smoother Alchemical Transformations via Enveloping Distribution Sampling for Free-Energy Estimation.Journal of chemical theory and computation · 2026Article
- Synthesis, Biological Evaluation, Molecular Docking and Molecular Dynamics of Substituted Thieno[2,3-d]pyrimidine Derivatives as Potential Anti-Alzheimer Agents.International journal of molecular sciences · 2026Article
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- Mechanochemical Decoupling of ATP Hydrolysis and RNA Translocation in SARS-CoV-2 nsp13 by the L405D Mutation.bioRxiv : the preprint server for biology · 2026Article
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- Comparative insecticidal efficacy and biochemical impact of nano-encapsulated citronella and geranium essential oils against Spodoptera littoralis (Lepidoptera: Noctuidae).Scientific reports · 2026Article
- Pathway Representation via Intrinsic Structural Medoids (PRISM): A Structural Mapping Approach to Clustering Molecular Pathways.bioRxiv : the preprint server for biology · 2026Article
- Click chemistry of phenyl 1,2,3-triazole-2-pyridylpiperazine hybrids: synthesis, targeted anticancer activity, molecular modeling and computational studies.RSC advances · 2026Article
- Article
- H2A.Z facilitates Sox2-nucleosome interaction by promoting DNA and histone H3 tail mobility.Nucleic acids research · 2026Article
- MD Simulation of Vector-Receptor Pharmacologic Pairs for Tumor-Specific Drug Delivery: Transfer of Boron Atoms by RGD Peptide to αvβ3 Integrin Receptor.Current issues in molecular biology · 2026Article
164 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
Abstract
We report progress in graphics processing unit (GPU)-accelerated molecular dynamics and free energy methods in Amber18. Of particular interest is the development of alchemical free energy algorithms, including free energy perturbation and thermodynamic integration methods with support for nonlinear soft-core potential and parameter interpolation transformation pathways. These methods can be used in conjunction with enhanced sampling techniques such as replica exchange, constant-pH molecular dynamics, and new 12-6-4 potentials for metal ions. Additional performance enhancements have been made that enable appreciable speed-up on GPUs relative to the previous software release.
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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.