The Java Essential Dynamics inspector (JEDi) software is a major upgrade from the previous JED software. Results Employing multi-threading, JEDi features a user-friendly interface to control rapid workflows for
Molecular dynamicsComputer simulationThe relative performance of molecular dynamics (MD) computer simulations of fluids written in ANSI C is compared to that achieved by a comparable program written in Java. The performance of the Java program is shown to be dependent upon its runtime environment. ...
and molecular dynamics simulations were carried out using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS, version Sep2021)57, as well as using the Discover program. OVITO1012.8, VMD102, the Multiwfn103software, and Materials Studio were employed to visualize MD trajectories and ...
With Java Essential Dynamics (JED) as a forerunner, the JEDi software includes novel hierarchical PCA methodologies, more statistical tools and multithreading is added to achieve real-time analysis. JEDi handles high throughput analysis involving large numbers of input files simultaneously for comparative ...
According to molecular dynamics simulations, the low friction of both low- and high-coverage SAMs originates from the mobility of interfacial water molecules. These findings reveal a yet unknown and counterintuitive mechanism for slipperiness, opening new avenues for enhancing the mobility of droplets....
AlphaFold2 Modeling and Molecular Dynamics Simulations of the Conformational Ensembles for the SARS-CoV-2 Spike Omicron JN.1, KP.2 and KP.3 Variants: Mutational Profiling of Binding Energetics Reveals Epistatic Drivers of the ACE2 Affinity and Escape Hotspots of Antibody Resistance by Nishank Ra...
The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98 and ff99), CHARMM (19 and 27), Al...
Setting up and running molecular dynamics simulations of membrane proteins Methods, 41 (2007), pp. 475-488 View PDFView articleView in ScopusGoogle Scholar [157] M. Javanainen Universal method for embedding proteins into complex lipid bilayers for molecular dynamics simulations J. Chem. Theory Comp...
Jdpd - An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics - zielesny/Jdpd
All-atom (AA) molecular dynamics simulations were performed with the GROMACS simulation package41. The selected force field for AA in the simulation system is the OPLSS-AA force field, and the SPC/E model was used for water molecules as solvent42. The simulation initially started with energy...