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 interrogating conformational motions of biopolymers at various spatial resolutions and within ...
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. ...
The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 ( http://cgmartini.nl ), with an improved interaction balance, new bead types and expanded ability to include specific interac
第一步 安装 Tomcat Tomcat7需要安装在Java目录下,并进行配置 第二步 1.打开Eclipse,选择菜单栏的file》New》Dynamic Web Project 弹出窗口如下 2.点击Next》Next进入下面界面: 3.想要生成web.xml,就把Generate web.xml deployment descriptor前的选择框打勾 然后点击Finish,一个java W...Linux...
Principal component analysis (PCA) is commonly applied to the atomic trajectories of biopolymers to extract essential dynamics that describe biologically relevant motions. Although application of PCA is straightforward, specialized software to facilitate
Molecular dynamics (MD) simulation is a widely used computational tool to explore relationships between structure, dynamics, and function of biomolecules [13], [14], [15], [16]. It has been applied to a wide variety of biomolecules, in particular proteins [17], [18], [19], nucleic ...
DL_POLY Classic is a general purpose molecular dynamics simulation package that can run in parallel and includes a Java graphical user interface. GALAMOST (GPU accelerated large-scale molecular simulation toolkit) uses GPU computing to perform traditional molecular dynamics with a special focus on polym...
Jdpd - An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics - zielesny/Jdpd
uncoated areas of the substrate well beyond the size of a water molecule as probed by metal reactants. 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 ...
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 16, 673–683 (2008). CAS PubMed PubMed Central Google Scholar Brunger, A. T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta ...