VMD

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Contents [hide] 1 Description 2 Home page 3 Source code 4 Executables 5 Supported platforms 6 Documentation 7 Useful tricks 8 Contact information 9 See also

Description

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. It is one of the most user-friendly programs available for this purpose. It is particularly useful for visualizing trajectories, either, e.g., in Charmm (.DCD) or PDB (MODEL ... ENDMDL) formats.

Home page

• http://www.ks.uiuc.edu/Research/vmd/

Source code

• http://www.ks.uiuc.edu/Research/vmd/

Executables

Supported platforms

Documentation

• http://www.ks.uiuc.edu/Research/vmd/current/docs.html

Useful tricks

• To vizualize a trajectory, do:
  • vmd structure.pdb
  • In the "VMD main" window, select your molecule.
  • In the File menue, select "Load data into Molecule"
  • Browse and select your trajectory file
  • If it is not recognized automatically, you may have to specify the correct file format
  • To animate your structure, click on the arrow at the bottom-right of the "VMD main" window
  • Enjoy

• To generate a Charmm trajectory (.DCD) from a series of PDB files, you may use Catdcd as follows:
  • cat *.pdb > file_all.pdb
  • catdcd -o file_all.dcd -pdb file_all.pdb

• You may need to do this with a specified order for the PDB files. For instance, to have their order given by the date of the files:
  • cat `ls -t *.pdb` > file_all.pdb
  • catdcd -o file_all.dcd -pdb file_all.pdb

Contact information

vmd@ks.uiuc.edu

See also

• NAMD - NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.

• Software