[MMTK] NMA question

vanitha@cs.wisc.edu vanitha at cs.wisc.edu
Thu Mar 23 16:36:18 CET 2006

> A comment on the normal modes (step 5): Since the two molecules do
> not interact, you will have a total of 12 zero-energy modes (the
> translation and rotation of the two molecules). Any other mode will
> contain a deformation of only one of the two molecules, except if the
> two molecules are identical (in that case there are degenerate
> modes). So even though you calculate the modes for the two molecules
> together, you can still separate them into deformations of the
> individual molecules, which I think is what you want.

1) The version of MMTK I have does not have a method called
EnergeticModes(..). How is this different from NormalModes(..)?

2) Also, if I'm understanding you correctly here, if one of the molecules
has M atoms and the other has N atoms, then I'm going to end up with a
3(N+M) x 1 vector. In what order will these be in? Would there be a
one-to-one correspondence between the gradient of the force field with
respect to the co-ordinates of the molecules and the normal mode vectors?
I just want to to make sure that I'm not adding apples & oranges :-)

3) I just need the first few non-trivial modes to begin with. Do you know
if there is a way to compute just these and save MMTK the trouble of
having to compute them all?


- Vanitha

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