[MMTK] calculate RMSD of a collection of atoms from trajectory

Shirley Siu siu at mpi-sb.mpg.de
Tue Mar 15 18:49:18 CET 2005


Dear list,

I would like to calculate the RMSD of some atoms from the trajectory,
using the first frame as the reference. However, the result showed only
very little different and it is suspicious. I wonder if my way of
doing it is correct or not.

---
... load the trajectory...

universe=trajectory.universe
proteins=universe.objectList(Protein)
collect=proteins[1]  # only calculate RMSD for chain 1
reference=self.trajectory.configuration[0]

for step in self.trajectory[1:]:
    tr,rms=collect.findTransformation(step['configuration'],reference)
    print rms

The RMSD ranges from 0 to less than 0.3 over all the frames.

Thanks in advance.

Siu

"Art is the lie that helps tell the truth..."     ^o^ Pablo Picasso



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