Desmond Tutorial

Desmond Tutorial
Analyzing Trajectories Using VMD
# Scale the average
avg /= n
Big trajectories
It is often the case that not all frames of a trajectory can fit into memory at once. The
BigTrajectory framework provided by the Desmond distribution makes it simple to
circumvent this limitation for analysis scripts that need to process just one frame at a
time.
In order to use BigTrajectory, the user writes one or more analysis tasks that implement
a processFrame() method like the one described in the previous section. BigTrajectory
then takes care of looping through snapshots one at time and calling each
task in turn to process the data.
Any number of reference frames can be kept in memory while the trajectory frames are
processed, so that tasks like RMSD alignment can be implemented. Organizing your
analysis code into tasks encourages module code development and reuse. Figure 9.5
shows how, with only trivial changes, the script in Figure 9.4 on page 93 can be adapted
to be used in BigTrajectory.
Figure 9.5 Analysis task using BigTrajectory
##
## file: Analysis.py
##
from atomsel import atomsel
import molecule, vmdnumpy
import numpy
import BigTrajectory
class AnalysisTask:
def __init__(self, rmsfile):
self.avg = None
# will hold averaged coordinates
self.count = 0
# number of processed frames
self.all = atomsel() # all atoms in current frame
self.ref = atomsel('name CA', frame=0) # reference frame is
frame 0
self.sel = atomsel('name CA') # alpha carbons in current frame
self.inds = sel.get('index')
self.mass = sel.get('mass')
# write initial 0 to rmsfile output
self.rmsfile.write("%f\n" % 0)
def processFrame(self):
# Align current frame with reference frame
self.all.move( self.sel.fit(self.ref, self.mass) )
# Write out next value of RMSD
self.rmsfile.write( "%f\n" % self.sel.rmsd(self.ref, self.mass) )
94 D. E. Shaw Research September 2008