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Following is a list of TCL scripts that can be executed with VMD using “vmd -dispdev text -e *.tcl”. They can be used to prepare systems for NAMD simulations and analyze simulation output trajectories, notably on viral capsids.

A TCL script used to take a set of .ppm images renderred with VMD (“Extensions” -> “Visualization” -> “Movie Maker”), resize/crop the images, add time, and then generate a .gif animation.


Sample input file for running AddTime2VMDmovie.tcl

A test example for running AddTime2VMDmovie.

Generate the .psf and .pdb files from input PDB structure, solvate the structure in water and ionize the system with VMD to prepare the system for simulation.


1) Analyize the changes in the radii of viral capsid backbone, i.e., the average, maximum and minimum distances between atoms in the capsid backbone and the capsid center of mass, in a simulation trajectory.

2) Calculate the RMSD between viral capsid snapthots along simulation trajectory and a reference structure.

Calculate the interior, exerior and total SASA of viral capsids from a simulation trajectory.

Calculate the volume of a viral capsid and that inside the capsid cavity. In case the capsid is solvated in a water box, the volume of the host medium outside of the capsid is also calculated.

Calculate the density of water inside viral capsid cavity and that outside of the capsid by using the volume data obtained from executing script “analysis-capsidvolume.tcl”.

Analyize the rigid-body translation and rotation of capsomeres (i.e., pentamers and hexamers) in CCMV capsid.