ArticleThe journal of physical chemistry. B2024
Introductory Tutorials for Simulating Protein Dynamics with GROMACS.
Article in The journal of physical chemistry. B, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 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
60 citing papers in PubMed.
- Evolutionary and structural pathways of antibody maturation reveal principles for engineering potent SARS-CoV-2 neutralizers.Journal of structural biology: X · 2026Article
- Site-specific O-glycans influence lacritin structure and multimerization in tears.Protein science : a publication of the Protein Society · 2026Article
- Structure-Based Design and Evaluation of Coumarin-Derived CDK4 Inhibitors for Non-Small Cell Lung Cancer: An Integrated Computational Study.Applied biochemistry and biotechnology · 2026Article
- Stabilization of Bone Morphogenetic Protein-2 at Physiological pH: Contrasting Roles of CHAPS and Arginine in Aggregation Inhibition.Proteins · 2026Article
- Identification of potential SARS-CoV-2 MJournal of computer-aided molecular design · 2026Article
- Which Metrics Best Capture Protein Structural Changes in Molecular Dynamics Simulations? Evaluating Score Combinations and Force-Field Effects.Journal of chemical information and modeling · 2026Article
- Cinerascensosides A and B, Two New Cytotoxic Sulfated Saponins From the Sea Cucumber Holothuria cinerascens.Chemistry & biodiversity · 2026Article
- A Novel Sulfatide Analog Recognized by Human iNKT Cells Enhances Polyfunctional Antigen-Specific CD8European journal of immunology · 2026Article
- Toward Relative Redox Potential Predictions in Flavoproteins: Treatment of a Charge-Changing Mutation in Alchemical Free Energy Simulations.Journal of chemical theory and computation · 2026Article
- Article
- Tutorial for Atomistic and Coarse-Grained Simulations of Membrane-Nanoplastic Interactions Using GROMACS.The journal of physical chemistry. B · 2026Article
- M2-PRNet: multi-scale and multi-modal learning for protein-RNA binding affinity prediction.Bioinformatics (Oxford, England) · 2026Article
- Coordination-controlled photophysics and antiproliferative activity of coumarin-linked schiff bases and Zn(II) complexes.Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology · 2026Article
- Curcumin Attenuates Decidual Stromal Cell Ferroptosis and Restores Impaired Decidualization in Recurrent Spontaneous Abortion by Targeting BRD4.Food science & nutrition · 2026Article
- Testican-1-MMP axis in tumour extracellular matrix (ECM) remodelling: interaction dynamics analysis and an in silico perspective.The Journal of pathology · 2026Article
- Lipid Disorder and PIP2-Regulated Clustering of Syntaxin-1 JMD-TMD Regions Govern Membrane Fusion Competence.International journal of molecular sciences · 2026Article
- Thousandfold Expansion Microscopy.bioRxiv : the preprint server for biology · 2026Article
- AI-GuidedJournal of the American Chemical Society · 2026Article
- Mechanisms of Xiangxue decoction in treating COVID-19 via HPLC‒Q-TOF‒MS/MS, network pharmacology, molecular docking and molecular dynamics simulation.Scientific reports · 2026Article
- Enhancing the Antimicrobial Potency of Self-Assembling Antibiotics by Co-Assembly-Based Aggregation Modulation.Macromolecular bioscience · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
Abstract
Atomistic molecular dynamics (MD) simulations have become an indispensable tool for investigating the structure, dynamics, and energetics of biomolecules. Continual optimization of software algorithms and hardware has enabled investigators to access biologically relevant time scales in feasible amounts of computing time. Given the widespread use and utility of MD simulations, there is considerable interest in learning essential skills in performing them. Here, we present a set of introductory tutorials for performing MD simulations of proteins in the popular, open-source GROMACS package. Three exercises are detailed, including simulating a single protein, setting up a protein complex, and performing umbrella sampling simulations to model the unfolding of a short polypeptide. Essential features and input settings are illustrated throughout. The purpose of these tutorials is to provide new users with a general understanding of foundational workflows, from which they can design their own simulations.
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.