sgport.blogg.se - Networkview

#NETWORKVIEW UPDATE#
#NETWORKVIEW SOFTWARE#

Of CHARMM-compatible force field parameters FFTK - Tool to aid users in the development.Dowser - Add water to a structure for simulation, using Dowser.CGTools - Transform structures between coarse-grain and all-atom representations.Cispeptide - Detect, visualize, and fix cis peptide bonds in protein structures.Chirality - Detect and fix chirality errors in protain and nucleic acid structures.AutoPSF - Automatic PSF structure building tool.AutoIonize - Add sodium or chlorine ions to a structure for simulation.MultiText - Display and edit text files.PDBtool - Query various information about PDB structures.Multiplot - Scriptable data plotting tool.Data Import - Load per-residue values into the "beta" column of a PDB file.Shared VMD Views - Publish and view VMD states to/from other BioCoRE users.Login - Login to BioCoRE from within VMD.Chat - Chat with other BioCoRE users from within VMD.VolMap - Graphical front-end for the VMD VolMap command.Timeline - Plot time-varying secondary structure.Symmetry Tool - Determine the symmetry pointgroup of an atom selection and display the symmetry elements.Sequence Viewer - Browse sequences of loaded molecules.Salt Bridges - Find salt bridges throughout a trajectory.RMSD Visualizer Tool - Tool for aligning selections and measuring and plotting RMSD and RMSF values over trajectories.RMSD Trajectory Tool - Extended version of RMSD plugin for trajectories.RamaPlot - Ramachandran plots for selected atoms.PropKa GUI - graphical interface for PROPKA.PMEpot - Particle Mesh Ewald potential map calculator.ParseFEP - Analyze NAMD free-energy purturbation (FEP) Simulations.NMWiz - Normal mode visualization and comparative analysis.NetworkView - View protein interaction networks.NAMD Plot - Plot NAMD log files (energy/volume/.).NAMD Energy - Evaluate interaction energies with NAMD.MultiSeq - Perform multiple sequence and multiple structure alignments, display sequence data, phylogenetic trees, and much more.IRSpecGUI - IR spectral density calculator.ILSTools - Prepare and run Implicit Ligand Sampling (ILS) calculations.

HeatMapper - Plot 2-D heat maps of 3-D values with a color scale bar.

HBonds - Counts the number of hydrogen bonds formed over a trajectory.

GofRGUI - Calculate and plot radial pair distribution functions g(r).Contact Map - Plot a 2-d residue-residue distance map.CatDCD - Standalone trajectory processing program.APBSRun - Calculate electrostatic potentials using APBS.AlaScan - Automate alanine scanning for free-energy perturbation MD simulations.Documentation for all supported file formats, and translators Extensions Documentation: Analysis.

#NETWORKVIEW SOFTWARE#

Plugin Programmer's Guide - describes the VMD plugin architecture so others can develop and build new plugins, and to use the VMD plugins in other software.

#NETWORKVIEW UPDATE#

VMD 1.9.2 update for Gromacs plugins ().

This page contains plugins which can be downloaded and installed in yourĬopy of VMD, as well as any pertinent documentation that goes along withĪny exceptions are explicitly marked as such. Types of plugins for VMD are 'molfile' plugins for readingĪnd writing data files containing atomic, graphics, and volumetric data,Īnd scripting extensions which implement new commands and user interfacesįor performing tasks such as structure building, simulation setup, etc. Without the necessity to recompile the program. Interfaces which provide a means for extending VMD at run-time In addition to Tcl and Python scripts, VMD implements "plugin"