ArticleJournal of chemical information and modeling2016
TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.
Article in Journal of chemical information and modeling, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 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
34 citing papers in PubMed.
- Thermodynamic and Atomistic Insights into Lignin Solubility from Experimentally Validated Molecular Dynamics Simulations.Biomacromolecules · 2026Article
- Canthaxanthin downregulates EGFR in NSCLC: network pharmacology, molecular docking, dynamics simulations, ADMET, and in-vitro analysis.Molecular diversity · 2026Article
- Dynamics and Structural Responses to Cis-Trans Isomerization in Bacterial Lipid Bilayers.ACS omega · 2026Article
- Monosaccharide-Derived Enantioselectivity in SWCNT Chemoresistive VOC Sensing.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- gmx_ffconv: A Fast, User-Friendly Semi-Automated All-Atom Force Field Converter for GROMACS.Journal of chemical information and modeling · 2025Article
- Effect of Solvents on Lignin-Surface Interactions via Molecular Dynamics Simulations.The journal of physical chemistry. B · 2025Article
- Wood Biomolecules as Agricultural Adjuvants for Effective Suppression of Droplet Rebound from Plant Foliage.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Increasing thermostability of the key photorespiratory enzyme glycerate 3-kinase by structure-based recombination.Plant biotechnology journal · 2025Article
- PACKMOL-GUI: An All-In-One VMD Interface for Efficient Molecular Packing.Journal of chemical information and modeling · 2025Article
- Atomic view of photosynthetic metabolite permeability pathways and confinement in synthetic carboxysome shells.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Advanced Molecular Dynamics Model for Investigating Biological-Origin Microfibril Structures.ACS omega · 2024Article
- Multifaceted Activity of Fabimycin: Insights from Molecular Dynamics Studies on Bacterial Membrane Models.Journal of chemical information and modeling · 2024Article
- Understanding Lignin Dissolution with Urea and the Formation of a Lignin Nano-Aggregate: A Multiscale Approach.Nanomaterials (Basel, Switzerland) · 2024Article
- Predicting the Structure of Enzymes with Metal Cofactors: The Example of [FeFe] Hydrogenases.International journal of molecular sciences · 2024Article
- AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD.Journal of chemical information and modeling · 2024Article
- Development of substituted benzylidene derivatives as novel dual cholinesterase inhibitors for Alzheimer's treatment.RSC advances · 2023Article
- Article
- MD-Ligand-Receptor: A High-Performance Computing Tool for Characterizing Ligand-Receptor Binding Interactions in Molecular Dynamics Trajectories.International journal of molecular sciences · 2023Article
- A mini-TGA protein modulates gene expression through heterogeneous association with transcription factors.Plant physiology · 2023Article
- Current Trends and Changes in Use of Membrane Molecular Dynamics Simulations within Academia and the Pharmaceutical Industry.Membranes · 2023Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Molecular dynamics (MD) simulation engines use a variety of different approaches for modeling molecular systems with force fields that govern their dynamics and describe their topology. These different approaches introduce incompatibilities between engines, and previously published software bridges the gaps between many popular MD packages, such as between CHARMM and AMBER or GROMACS and LAMMPS. While there are many structure building tools available that generate topologies and structures in CHARMM format, only recently have mechanisms been developed to convert their results into GROMACS input. We present an approach to convert CHARMM-formatted topology and parameters into a format suitable for simulation with GROMACS by expanding the functionality of TopoTools, a plugin integrated within the widely used molecular visualization and analysis software VMD. The conversion process was diligently tested on a comprehensive set of biological molecules in vacuo. The resulting comparison between energy terms shows that the translation performed was lossless as the energies were unchanged for identical starting configurations. By applying the conversion process to conventional benchmark systems that mimic typical modestly sized MD systems, we explore the effect of the implementation choices made in CHARMM, NAMD, and GROMACS. The newly available automatic conversion capability breaks down barriers between simulation tools and user communities and allows users to easily compare simulation programs and leverage their unique features without the tedium of constructing a topology twice.
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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.