VMD

From MarcsHomepage

Introduction

VMD is a UNIX-based molecular viewer with OpenGL-interface, developed by the Theoretical Biophysics Group, University of Illinois. There are versions for OpenGL-accelerated workstations (SGI, Sun, DEC, as well as X-Window-versions (Linux). A port to Windows is also available. I have tested VMD under SuSE 5.1 and it worked quite good although it was even slower than Molmol and comparable OpenGL-based modellers and viewers.

VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

User Interface

Vmd1.jpg

The GUI is XForms-based, and can be integrated into other MD/modelling environments. The interface has several pop up-menus and a command-line and is completely customizable.

Dialogues pop up as non-modal windows, which can become a bit confusing, if you open a lot of them.

On the other hand, VMD is one of the most versatile and powerfull programs reviewed here, so it seems to be natural that you will need a longer time to get used to it.

In my opinion, Molmol or Pymol are still easier to use.

Features

(Taken from the VMD-homepage)

  • No limits on the number of molecules, atoms, residues or number of animation frames, excepting available memory.
  • Many molecular rendering and coloring methods.
    • Lines
    • Bonds
    • Cartoon
    • vdW
    • CPK, ball/stick
    • Licorice
    • Tube
    • Ribbons
    • Contact/solvent-accessible surface (solid/dotted)

For each of these representations, you may color by atom, residue, segment, molecule name, mass, charge, occupancy, position, and backbone.

  • Stereo display capability.
  • Extensive atom selection syntax for choosing subsets of atoms for display (includes boolean operators, regular expressions, and more).
  • Integration with the program 'Babel' which allows VMD to read many molecular data file formats. Even without the use of Babel, VMD can read PDB files, as well as CHARMM- and X-PLOR compatible binary DCD files and X-PLOR compatible PSF files.
  • Ability to write the current image to a file which may be processed by a number of popular raytracing and image rendering packages, including POV-Ray, Rayshade, Raster3D, and Radiance.
  • Extensive graphical and text-based user interfaces, which use the Tcl package to provide full scripting capabilities.
  • Extensions to the Tcl language which enable researchers to write their own routines for molecular analysis
  • Modular, extensible source code using an object-oriented design in C++, with a programmers guide describing the source code
  • Integration with the program NAMD, a fast, parallel, and scalable molecular dynamics program developed in conjunction with VMD in the Theoretical Biophysics Group at the University of Illinois. See the NAMD WWW home page for more info: http://www.ks.uiuc.edu/Research/namd/