Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
Herein we present the VMD Store, an open-source VMD plugin that simplifies the way that users browse, discover, install, update, and uninstall extensions for the Visual Molecular Dynamics (VMD) software. The VMD Store obtains data about all the indexed VMD extensions hosted on GitHub and presents a one-click mechanism to install and configure VMD extensions. This plugin arises in an attempt to aggregate all VMD extensions into a single platform. The VMD Store is available, free of charge, for Windows, macOS, and Linux at https://biosim.pt/software/ and requires VMD 1.9.3 (or later).
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1021/acs.jcim.9b00739 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
HydroLayer Calculator: A Pseudo-Parallel Tool for Rapid Hydration Layer Structure Calculation in MD Simulations via VMD.
J Chem Inf Model
August 2025
Key Laboratory of High Efficiency and Clean Mechanical Manufacture, Ministry of Education, School of Mechanical Engineering, Shandong University, Jinan 250061, P. R. China.
Hydration plays a crucial role in the performance of hydrophilic materials, influencing properties such as fouling resistance and lubrication. Characterizing the parameters of the hydration layer is essential to understanding these behaviors. In this study, we developed the HydroLayer Calculator, a multiparameter analysis tool based on Tcl, designed to calculate six key parameters of the hydration layer along the radial direction of the reference atoms using VMD: radial distribution function (RDF), orientation distribution function (ODF), hydrogen bond (HB) structure, mean square displacement (MSD), mean residence time (MRT), and water binding sites (WBS).
View Article and Find Full Text PDFPACKMOL-GUI: An All-In-One VMD Interface for Efficient Molecular Packing.
J Chem Inf Model
January 2025
Sino-Finland Joint AI Laboratory for Child Health of Zhejiang Province, Hangzhou 310052, China.
PACKMOL is a widely utilized molecular modeling tool within the computational chemistry community. However, its tremendous advantages have been impeded by the longstanding lack of a robust open-source graphical user interface (GUI) that integrates parameter settings with the visualization of molecular and geometric constraints. To address this limitation, we have developed PACKMOL-GUI, a VMD plugin that leverages the dynamic extensibility of the Tcl/Tk toolkit.
View Article and Find Full Text PDFHadron-ion collisions in Pythia and the vector-meson dominance model for photoproduction.
Eur Phys J C Part Fields
November 2024
Department of Physics, University of Jyvaskyla, P.O. Box 35, Fl-40014 Jyvaskyla, Finland.
Article Synopsis
- The extension of the Pythia Monte Carlo event generator allows for detailed simulations of collisions between a hadron beam and nuclear targets, with energy variations for each event.
- The work builds on existing models like Angantyr for heavy ions and includes a vector-meson dominance (VMD) model for simulating real photon interactions in photo-nuclear collisions.
- Validation with HERA data shows the model's effectiveness, and the generated events for ultra-peripheral heavy-ion collisions at the LHC align with ATLAS measurements, demonstrating consistency in single-particle multiplicity and azimuthal anisotropy patterns.
Serial Diffusion Tensor Imaging and Rate of Ventricular Blood Clearance in Patients with Intraventricular Hemorrhage.
Neurocrit Care
February 2025
Institute for Stroke and Cerebrovascular Diseases and Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, USA.
Background: We developed a noninvasive biomarker to quantify the rate of ventricular blood clearance in patients with intracerebral hemorrhage and extension to the ventricles-intraventricular hemorrhage.
Methods: We performed magnetic resonance imaging in 26 patients at 1, 14, 28, and 42 days of onset and measured their hematoma volume (HV), ventricular blood volume (VBV), and two diffusion metrics: fractional anisotropy (FA), and mean diffusivity (MD). The ipasilesional ventricular cerebral spinal fluid's FA and MD were associated with VBV and stroke severity scores (National Institute of Health Stroke Scale [NIHSS]).
Lambda-ABF: Simplified, Portable, Accurate, and Cost-Effective Alchemical Free-Energy Computation.
J Chem Theory Comput
June 2024
Laboratoire de Biochimie Théorique, Université Paris Cité, CNRS, UPR 9080, 75005 Paris, France.
We introduce the lambda-Adaptive Biasing Force (lambda-ABF) method for the computation of alchemical free-energy differences. We propose a software implementation and showcase it on biomolecular systems. The method arises from coupling multiple-walker adaptive biasing force with λ-dynamics.
View Article and Find Full Text PDF