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Academic literature on the topic 'Gromacs script'

Author: Grafiati

Published: 4 June 2025

Last updated: 1 August 2025

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Journal articles on the topic "Gromacs script"

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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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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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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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 "Supramolecular Semiconductivity through Emerging Ionic Gates in Ion−Nanoparticle Superlattices", published on ACS Nano (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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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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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: - Investigating the Aryl Hydrocarbon Receptor Agonist/Antagonist Conformational Switch using Well-Tempered Metadynamics Simulations 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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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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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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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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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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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 Carlesso, Antonio; Chintha, Chetan; Gorman, Adrienne; Samali, Afshin; Eriksson, Leif   Background 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 Contents There are eighte

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Dissertations / Theses on the topic "Gromacs script"

Sharir, Yacov. "Beyond the electronic connection : the technologically manufactured cyber-human and its physical human counterpart in performance : a theory related to convergence identities." Thesis, University of Plymouth, 2013. http://hdl.handle.net/10026.1/1498.

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This thesis is an investigation of the complex processes and relationships between the physical human performer and the technologically manufactured cyber-human counterpart. I acted as both researcher and the physical human performer, deeply engaged in the moment-to-moment creation of events unfolding within a shared virtual reality environment. As the primary instigator and activator of the cyber-human partner, I maintained a balance between the live and technological performance elements, prioritizing the production of content and meaning. By way of using practice as research, this thesis ar

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