Analyze Trajectories in VMD

Useful information can be found on the following websites:

Analyze your trajectory

  • Start VMD, open the Tk console and load the .gro file of the trajectory to analyze.
cd /Users/davidoppenheimer/Dropbox\ \(UFL\)/GROMACS/gromacs-prot-ligand-tutorial
mol new md_0_10.gro
  • Then load the trajectory file into the previously loaded molecule.
    • In the VMD Main window, select the molecule.
    • Go to File → Load Data into Molecule and choose the .xtc trajectory to load from the file browser. Or use the Tk console.
mol addfile {/Users/davidoppenheimer/Dropbox (UFL)/GROMACS/gromacs-prot-ligand-tutorial/md_0_10_fit.xtc} type {xtc} first 0 last -1 step 1 waitfor 1 0
  • Create a representation of the water molecule, and then hide it.
mol addrep 0 # add representation to molecule 0; this is rep 1
# modstyle rep_number molecule_number rep_style
mol modstyle 1 0 lines # rep 1, molecule 0
# modselect rep_number molecule_number select_method: Change the current selection for the given representation in the specified molecule.
mol modselect 1 0 water
# showrep molecule_number rep_number [on | off]
mol showrep 0 1 off
mol addrep 0
mol modselect 2 0 protein
mol modselect 3 0 resname JZ4
mol modstyle 3 0 vdw
mol showrep 0 0 off # turn off the "all" representation

Below are links to some useful programs to analyze trajectories.

Nice trajectory post-processing scripts: Advanced VMD: Trajectories, movies, scripting
MD-Task
MD-Task Documentation
MDAnalysis
STCSB
RIP-MD
webPSN v2.0
Geo-Measures This is a nice set of tools integrated into a PyMOL plugin.
Side-chain network approach

Not done yet! More to come.