ArticleJournal of chemical theory and computation2016
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.
Article in Journal of chemical theory and computation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2,213 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
2,213 citing papers in PubMed.
- Mechanistic studies on HNRNPA2B1 suggest binding but not selective recognition of mRNA biology · 2026Article
- Structural dynamics and pH-regulated membrane binding of the TRAF2-NC trimer.Protein science : a publication of the Protein Society · 2026Article
- Estimated Binding Affinities of Polyphenolic Compounds into the Human Peroxiredoxin 5 and the SARS-CoV-2 main Protease Binding Sites: In Silico Approach.Applied biochemistry and biotechnology · 2026Article
- Kinetic, computational, and phylogenetic characterisation of PA2125 from Pseudomonas aeruginosa PAO1: a hydroxybenzaldehyde dehydrogenase of the newly defined ALDH33 family.Bioscience reports · 2026Article
- SPRIZ (CCDC127) protein conserved in deuterostome animals is a rigid OMM-IMM tether that locally sets mitochondrial IMS volume.Science advances · 2026Article
- PI3Kδ is selectively inhibited by roginolisib by stabilizing the C-terminal helix kα12.Nature communications · 2026Article
- Lipid gating of BK channels and activation mechanism by negatively charged lipids.Communications chemistry · 2026Article
- Triazavirin And Its Derivatives Act As Influenza A Virus Fusion Inhibitors.Pharmaceutical research · 2026Article
- Integrated Experimental, Chemometric, and In Silico Analyses of Larvicidal Supercritical Extracts From Myrtaceae Species Against Aedes aegypti.Chemistry & biodiversity · 2026Article
- Understanding Biased Signaling and Small-Molecule Binding for Treatment of Type 2 Diabetes Mellitus and Obesity at the Glucagon-Like Peptide-1 Receptor (GLP-1R) Based on Molecular Dynamics Simulations.Medicinal chemistry research : an international journal for rapid communications on design and mechanisms of action of biologically active agents · 2026Article
- Design, synthesis, biological evaluation and computational studies of novel phthalimides as dual COX-2/5-LOX inhibitors.Molecular diversity · 2026Article
- Mechanism of GPR84 allosteric modulation at a helix 8-proximate site.Science advances · 2026Article
- Structural basis of stepwise G protein activation by the viral chemokine receptor US28.bioRxiv : the preprint server for biology · 2026Article
- Discovery of a new SARS-CoV-2 Mpro inhibitor from a natural product and natural product-like compound database using in silico and in vitro studies.Molecular diversity · 2026Article
- A Minimalist Model for Navigating Conformational Landscape Uncovers the Activation Mechanism of βACS physical chemistry Au · 2026Article
- Interpreting human genetic variation at atomic resolution.Nature genetics · 2026Review
- Benzamides of 2-(aminophenyl)benzimidazoles and 2-(aminophenyl)indoles as Anticancer Scaffolds: Synthesis, In Silico and In Vitro Evaluation.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Cryo-EM structures of Candida albicans chitin synthase Chs1 reveal a druggable translocation channel.Nature microbiology · 2026Article
- Subdomains of endophilin can drive membrane remodeling and facilitate controlled membrane scission.Biophysical journal · 2026Article
- Fast-Forward: Automatic Assignment and Assessment of Bonded Parameters for the Martini Force Field.Journal of chemical information and modeling · 2026Article
2,153 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors.
Funding
Abstract
Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.