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Journal articles on the topic 'Gromacs script'

Author: Grafiati

Published: 4 June 2025

Last updated: 15 July 2025

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1

Sinelnikova, Anna, and David van der Spoel. "NMR refinement and peptide folding using the GROMACS software." Journal of Biomolecular NMR 75, no. 4-5 (2021): 143–49. http://dx.doi.org/10.1007/s10858-021-00363-z.

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AbstractNuclear magnetic resonance spectroscopy is used routinely for studying the three-dimensional structures and dynamics of proteins and nucleic acids. Structure determination is usually done by adding restraints based upon NMR data to a classical energy function and performing restrained molecular simulations. Here we report on the implementation of a script to extract NMR restraints from a NMR-STAR file and export it to the GROMACS software. With this package it is possible to model distance restraints, dihedral restraints and orientation restraints. The output from the script is validat

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2

Ries, Benjamin, Salomé Rieder, Clemens Rhiner, Philippe H. Hünenberger, and Sereina Riniker. "RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology." Journal of Computer-Aided Molecular Design 36, no. 3 (2022): 175–92. http://dx.doi.org/10.1007/s10822-022-00445-6.

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AbstractThe calculation of relative binding free energies (RBFE) involves the choice of the end-state/system representation, of a sampling approach, and of a free-energy estimator. System representations are usually termed “single topology” or “dual topology”. As the terminology is often used ambiguously in the literature, a systematic categorization of the system representations is proposed here. In the dual-topology approach, the molecules are simulated as separate molecules. Such an approach is relatively easy to automate for high-throughput RBFE calculations compared to the single-topology

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3

Armeev, Grigoriy, Anastasiia Kniazeva, Galina Komarova, Mikhail Kirpichnikov, and Alexey Shaytan. "Abstract P-19: 15-Microsecond Molecular Dynamics Simulations of Nucleosome Show Structural Heterogeneity and Plasticity." International Journal of Biomedicine 11, Suppl_1 (2021): S19—S20. http://dx.doi.org/10.21103/ijbm.11.suppl_1.p19.

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Background: Nucleosomes are basic units of chromatin organization, resembling spools with ~150 base pairs of DNA wrapped around the octamer of histone proteins. They play a crucial role in chromatin compactization and gene expression. Currently, there are more than 340 structures of nucleosomes and their complexes with proteins in the protein data bank, 159 of them are made with cryoEM, 60 of those in 2020 and later. It is clear that cryoEM will soon yield even more structures of nucleosomes with different histone variants, mutations, DNA sequences, and interacting proteins. Despite the variet

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4

Lionello, Chiara, Claudio Perego, Andrea Gardin, Rafal Klajn, and Giovanni M. Pavan. "Research data on: "Supramolecular Semiconductivity through Emerging Ionic Gates in Ion−Nanoparticle Superlattices"." December 14, 2022. https://doi.org/10.5281/zenodo.7437648.

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This repository contains the set of data shown in the paper "<em><strong>Supramolecular Semiconductivity through Emerging Ionic Gates in Ion−Nanoparticle Superlattices</strong></em>", published on <strong><em>ACS Nano</em></strong> (DOI: 10.1021/acsnano.2c07558). All the input data needed to run the simulations and get the results are organized in 2 different folders:  * `1 - CoarseGrainedSimulations/`     in this folder there are all the Gromacs input files necessary to reproduce the coarse-grained simulations shown in the article. &nbsp

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5

Patrik, Nikolić, Turalija Matea, and Miletić Vedran. "Multistep High-Throughput Virtual Screening of 36 Million Commercially Available Compounds for the Identification of Novel Inhibitors Targeting SARS-CoV-2 Main Protease." December 31, 2021. https://doi.org/10.5281/zenodo.5854978.

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The data includes: output from the structure filtering protocol performed with RDKit using a Python script, input, intermediate, and output data for all molecular docking simulations done with RxDock (initial, second, and final pass), and all trajectories and associated data for compounds simulated with GROMACS and presented in the paper.

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6

Farag, Mosa, AlRawashdeh Sara, Ayman El-Kadi Dr., and Khaled Barakat Dr. "Investigating the Aryl Hydrocarbon Receptor Agonist/Antagonist Conformational Switch using Well-Tempered Metadynamics Simulations input and output files." June 19, 2023. https://doi.org/10.5281/zenodo.8401216.

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The MD simulation data for the research article: - <em>Investigating the Aryl Hydrocarbon Receptor Agonist/Antagonist Conformational Switch using Well-Tempered Metadynamics Simulations</em> Standard_md_files-GAFF.zip: The Standard_md folder comprises the initial conformations and prepared system files for both apo proteins and ligand-protein complexes. It also includes all topology files and coordinate files (.prmtop & .rst7) required for each system. Amber_md_input.zip: The Amber_input folder encompasses a comprehensive set of input files for the Amber to run molecular

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7

Staniscia, Fabio. "Cylindrical droplets analysis." May 29, 2023. https://doi.org/10.5281/zenodo.7982303.

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Python script to analyze the density profile of cylindrical droplets. It analyzes 2D density files '.dat', generated by GROMACS tool 'gmx densmap', in which density has been averaged over one spatial direction and time, to extract relevant physical quantities. First it divides the droplet density plot in three regions: an external one, an internal one, which correspond to the droplet bulk, and an interfacial one. Then it divides in interfacial region in three new parts: the water-vapor interface, the water-substrate interface and the contact line region. Analyzing them separate

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8

Vasiliki, Vakali, Papadourakis Michail, Georgiou Nikitas та ін. "Comparative Interaction Studies of Quercetin with 2-Hydroxyl-propyl-β-cyclodextrin and 2,6-Methylated-β-cyclodextrin". 5 серпня 2022. https://doi.org/10.5281/zenodo.6967424.

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Quercetin is a well-known natural product that can exert beneficial properties on human health. However, due to its low solubility its bioavailability is limited. In the present study, Here, we examine whether its formulation with two cyclodextrins (CDs) may enhance its pharmacological profile. Comparative interaction studies of quercetin with 2-hydroxyl-propyl-β-cyclodextrin (2HP-β-CD) and 2,6-methylated cyclodextrin (2,6Me-β-CD) were performed using NMR spec-troscopy and Molecular Dynamics (MD) simulations. Using T1 relaxation experiments and 2D DOSY it was illustrated that bo

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9

Suparna, Ghosh, Keretsu Seketoulie, and Joo Cho Seung. "Designing of the ROCK1 inhibitors." July 7, 2021. https://doi.org/10.5281/zenodo.5077971.

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Title: Designing of the N-ethyl-4-(pyridin-4-yl)benzamide based potent ROCK1 inhibitors using Docking, Molecular Dynamics, and 3D-QSAR The ZIP file contains all the protein-ligand docked complex, input/output files, ligand topology-parameter files, forcefield, and running scripts used on the above study.

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10

Carlesso, Antonio, Chetan Chintha, Adrienne M. Gorman, Afshin Samali та Leif A. Eriksson. "Structural distortions induced by Kinase Inhibiting RNase Attenuator (KIRA) compounds prevent the formation of face-to-face dimers of Inositol Requiring Enzyme 1α". 19 серпня 2019. https://doi.org/10.5281/zenodo.3368654.

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<strong>Data Set: Structural distortions induced by Kinase Inhibiting RNase Attenuator (KIRA) compounds prevent the formation of face-to-face dimers of Inositol Requiring Enzyme 1α</strong> Carlesso, Antonio; Chintha, Chetan; Gorman, Adrienne; Samali, Afshin; Eriksson, Leif   <strong>Background</strong> Equilibration, relaxation and production runs were performed on CPUs using the GROMACS 5.1 version using AMBER ff14SB force field for the protein and GAFF for the small organic molecules. All software is available from http://www.gromacs.org <strong>Contents</strong> There are eighte

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11

SADID, Muhammad Maulana, and Moh Sofi’ul ANAM. "Anti-methanogenic effect of pyrogallol in Spirulina platensis – molecular docking and dynamics simulation on methyl-coenzyme M reductase." Journal of Life Science and Biomedicine, September 25, 2024, 45–53. http://dx.doi.org/10.54203/jlsb.2024.5.

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Methane, along with carbon dioxide and nitrogen oxides, is a key greenhouse gas contributing significantly to the global concern over climate change. This study investigated the anti-methanogenic properties of pyrogallol in Spirulina platensis using molecular docking and dynamics simulation on methyl-coenzyme M reductase (MCR). The Swiss ADME web server was used to identify pyrogallol's absorption, distribution, metabolism, and excretion (ADME) properties. Molecular docking studies were conducted using UCSF Chimera with the Vina script as the executor. The docking results were further analyzed

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12

Woods, Christopher J., Lester O. Hedges, Adrian J. Mulholland, et al. "Sire: An interoperability engine for prototyping algorithms and exchanging information between molecular simulation programs." Journal of Chemical Physics 160, no. 20 (2024). http://dx.doi.org/10.1063/5.0200458.

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Sire is a Python/C++ library that is used both to prototype new algorithms and as an interoperability engine for exchanging information between molecular simulation programs. It provides a collection of file parsers and information converters that together make it easier to combine and leverage the functionality of many other programs and libraries. This empowers researchers to use sire to write a single script that can, for example, load a molecule from a PDBx/mmCIF file via Gemmi, perform SMARTS searches via RDKit, parameterize molecules using BioSimSpace, run GPU-accelerated molecular dynam

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13

Suparna, Ghosh, Keretsu Seketoulie, and Joo Cho Seung. "Supplementary Files of 'Computational Modeling of FLT3 inhibitors'." July 13, 2021. https://doi.org/10.5281/zenodo.5664240.

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Title: Molecular modeling studies of <em>N</em>-phenylpyrimidine-4-amine derivatives for inhibiting FMS-like tyrosine kinase-3 The ZIP file contains all the protein-ligand docked complex, input/output files, ligand topology-parameter files, force field, and running scripts used in the above study.

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14

Panagopoulos, Papageorgiou Panagiotis, Katerina S. Karadima, Ioanna Papageorgiou, and Vlasis G. Mavrantzas. "Structural properties and conformational dynamics of keratin-derived antimicrobial peptides from molecular dynamics simulations." October 10, 2024. https://doi.org/10.5281/zenodo.13913344.

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The molecular dynamics simulation calculations were performed using GROMACS for KAMP-10, KAMP-10G2A, KAMP-18C, KAMP-18N, KAMP-19scr, KAMP-36, and Pw-Antibac12<sub>3</sub>. All related data can be found in the zipped folder named "Panagopoulos-Papageorgiou_etal_all_data.zip". In this zipped folder, there are two main folders named “Dilute solutions” and “Semi-dilute solutions”. Within these two main folders, there are subfolders where the data are located. These subfolders are named after each peptide. With regard to the dilute solutions, each of these subfolders include

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15

Hoffmann, Markus M., Matthew D. Too, Nathaniel A. Paddock, et al. "On the Behavior of the Ethylene Glycol Components of Polydisperse Polyethylene Glycol PEG200." January 16, 2023. https://doi.org/10.1021/acs.jpcb.2c06773.

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16

Xiaoyu, Wang. "Solvent Effects on Extractant Conformational Energetics in Liquid-Liquid Extraction: A Simulation Study of Molecular Solvents and Ionic Liquids." January 23, 2023. https://doi.org/10.5281/zenodo.8378117.

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17

Anton, Jansen, Bauer Paul, J. Howard Rebecca, Hess Berk, and Lindahl Erik. "Constant-pH molecular dynamics simulations of a proton-gated ion channel." March 25, 2024. https://doi.org/10.5281/zenodo.10869766.

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<strong>Constant-pH molecular dynamics simulations</strong> .analysis_results - Analysis (.csv) data and Python scripts for generating the (relevant) paper figures. .prep_file - Topology, force field, and GROMACS parameter files for preparing the simulations. .production_traj - Simulation trajectories and lambda coordinates.

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18

Grigory, Maksaev, Bründl-Jirout Michael, Stary-Weinzinger Anna, Zangerl-Plessl Eva-Maria, Lee Sun-Joo, and G. Nichols Colin. "Subunit gating resulting from individual protonation events in Kir2 channels." June 21, 2023. https://doi.org/10.5281/zenodo.8059438.

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Data to the paper "Subunit gating resulting from individual protonation events in Kir2 channels" accepted in Nature Communications. Molecular Dynamics simulation data for all 4 setups are provided. For each run, a compressed gromacs trajectory (.xtc, dt=1ns), the starting conformation (.pdb) and a .tpr file have been uploaded. Furthermore, we provide the scripts to generate the ions/waters over time plots.

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19

Hradiská, Helena, Martin Kurečka, Jan Beránek, et al. "Acceleration of Molecular Simulations by Parametric Time-Lagged tSNE Metadynamics - 2." August 14, 2023. https://doi.org/10.5281/zenodo.8246334.

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Supplementary files (trajectories, scripts for analysis and generation of images and other data). Data for metadynamics with two parametric time-lagged tSNE collective variables are in the mtd1 directory. Data for metadynamics with two parametric time-lagged tSNE collective variables and alphaRMSD are in the mtd2 directory. Data for parallel tempering metadynamics with two parametric time-lagged tSNE collective variables are in the ptmtd directory. Data for reference parallel tempering simulations are in the pt directory. The results were obtained by Gromacs (2021.4, 2021), Plumed (2.8.0, 2.9.

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20

Maxim, Zaigraev, and Chugunov Anton. "Membrane-mediated interaction of non-conventional snake three-finger toxins with nicotinic acetylcholine receptors." November 15, 2022. https://doi.org/10.5281/zenodo.7322819.

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Supplementary Data is stored in the MD-files.rar, Contacts.zip and RMSD.zip directories. 1) <strong>MD-files.rar</strong> contains molecular dynamics trajectories, system topologies and molecular dynamics parameters for GROMACS software package (<em>gro</em>, <em>xtc</em>, <em>itp </em>and <em>tpr</em> files). 2)<strong> Contacts.zip</strong> contains the obtained data on intermolecular interactions of WTX molecules with nicotinic receptor and membrane lipids. This folder includes  tables (<em>xlsx</em> and <em>csv </em>files) and python scripts utilized for

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21

Grothaus, Isabell Louise, and Jana Rosenau. "N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity." November 11, 2021. https://doi.org/10.5281/zenodo.6102786.

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New in version 3: Elongated trajectories for MD simulations of TconTS1 variants in complex with 3'SL as substrate. Revised MALDI-TOF data with raw spectra lists (including m/z, intensity and S/N) for all samples in Excel files. Directory for raw data files, as well as for files from molecular dynamics simulation of our publication "N-glycosylation of Trypanosoma congolense trans-sialidase modulates enzymatic activity" This archive contains two zip files, for raw data of MALDI-TOF mass spectrometry and for circular dichroism experiments. They contain subfolders for the d

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22

Crean, Rory, and Lynn Kamerlin. "KIF – Key Interactions Finder: A Program to Identify the Key Molecular Interactions that Regulate Protein Conformational Changes." October 1, 2022. https://doi.org/10.5281/zenodo.7104965.

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Starting structures, input files, analysis scripts and datasets used corresponding to the article: <em>KIF – Key Interactions Finder: A Program to Identify the Key Molecular Interactions that Regulate Protein Conformational Changes</em>. <strong>Further details (Same as in the readme file) are provided below:</strong> Note 1. the formatting of this document may look odd if you do not have "word wrap" switched on in your text editor.  Note 2. Both the MD simulations and PyContact calculations were run on computer clusters running Slurm Workload Manager. (So if you see any .

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