Desmond Tutorial

Analyzing Trajectories Using VMD
Getting information about snapshots
molecule.read(molid, filetype='dtr', filename='trajectory,dtr', waitfor=-
1)
The —1 argument to molecule.read indicates that a new molecule should be created
for the file. We specify filetype and filename to load the structure. Finally, we use the
molid returned by the first read command as the first argument to the second read command
so that data from the trajectory gets appended to the original structure file. The
waitfor=-1 means to load all frames in the trajectory before returning from the call. This
corresponds to the ‘Load all at once’ option in the File menu.
You can also specify a range of frames to be loaded:
molecule.read(molid, 'dtr', 'trajectory.dtr',
beg=5, end=55, skip=10, waitfor=-1)
Assuming there were at least 55 snapshots in trajectory.dtr, this command would
load snapshots 5, 15, 25, 35, 45, and 55 into the molecule with the given molid.
Getting information about snapshots
Data in VMD is organized into Molecules, which represent entire molecular systems as
well any number of snapshots associated with those systems. As molecules are loaded,
they are assigned a integer key called a molid. Exactly one molecule at any given time is
tagged as the top molecule; unless you set the top molecule yourself, this will always be
the most recently loaded molecule.
Each molecule in VMD has a fixed number of atoms. To each atom, VMD associates various
attributes such as name, type, mass, charge, etc. This data is usually obtained from a
structure file, but missing values not supplied by the structure file are guessed, and the
stored values can be overridden using scripting commands as described below.
The snapshots associated with each molecule are referred to as frames. Each frame holds
one set of coordinates for each atom in the molecule, as well as unit cell dimensions for
that frame. Velocities can also be stored if the trajectory file supplies them and the user
requests it using the appropriate file type. Table 1 summarizes the functions in the molecule
module for querying the high level structure of molecules in VMD.
In the rest of this section, we outline the Python interface provided by VMD to extract
atom and frame information from a molecule.
Atom selections
An atom selection consists of all the atoms in a particular molecule and frame that satisfy
some predicate, or set of conditions. We often refer to the predicate as the selection, but it
should be kept in mind that the set of atoms satisfying the predicate could be different for
different frames. Atom selections are used in the GUI to select which atoms to draw with
each style. The same selection language is used in the scripting interface to specify a predicate
for an atom selection object.
Atom selection objects are created in the VMD Python interface using the atomsel module:
# Import the atomsel type
from atomsel import atomsel
# Create a selection corresponding to all atoms in the top molecule,
September 2008 D. E. Shaw Research 89