VMD

VMD is a molecular visualization program installed on all workstations and clusters. The official documentation can be found here with some tutorials here. Like gnuplot however, the wealth of options means that often it takes a long time to find the one command you need to use so below you will find some useful basic settings/info for using VMD. For producing graphics for publication, Pymol is probably a better option as it has a built in ray-tracing routine but for general visualization, VMD is much quicker.

It is possible to load most files using command line flags, making loading many frames into different topology files easy. The -f flag indicates that all subsequent files (until the next -f flag or the end) should be loaded into a single molecule. There are also flags for selecting different file types (default is .pdb), most commonly parm7 for topology files generated by Amber and rst7 for restart files generated by Amber. mdcrd files are denoted -crd and periodic mdcrd files -crdbox.

e.g.

       vmd -f first_mol.pdb \
           -f -parm7 second_mol.prmtop -rst7 second_mol.rst \
           -f -parm7 third_mol.prmtop -crdbox third_mol_1st_frames.crd -crdbox third_mol_2nd_frames

Tutorials

• using VMD to display and manipulate '.pdb' files
• loading coordinate files into VMD with the help of an AMBER topology file e.g. to visualise the results of a GMIN run using AMBER9
• making movies from a '.pdb' file containing multiple structures. This is dealt with in the OPTIM section as part of the tutorial on making a movie of a path
• visualising normal modes using VMD and OPTIM