[MMTK] NMA question

Konrad Hinsen konrad.hinsen at cea.fr
Thu Mar 23 17:28:00 CET 2006


On Mar 23, 2006, at 16:36, vanitha at cs.wisc.edu wrote:

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

EnergeticModes is in MMTK 2.5. Just use NormalModes with 2.4 (which  
is VibrationalModes in 2.5 terminology).

> 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

The order depends on how you construct the system, on your Python  
version, on your MMTK version, and perhaps even more. Better don't  
make any assumption about atom oder. You don't need to.

> 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?

Yes, obviously. Everything done within one universe has that  
universe's atom order.

> I just want to to make sure that I'm not adding apples & oranges :-)

You would get an arror message if you tried :-)

> 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?

Yes, but you will save time and memory only if your system is quite  
big. There are two options:

1) Use an iterative eigenvector algorithm to obtain the first few  
modes. Those are the same modes as with a standard calculation. This  
is of interest mainly if you are running into memory limitations.  
Time-wise it rarely gives a substantial advantage.

2) Use a subspace (e.g. FourierSubspace). A well-chosen subspace will  
give you a good approximation to the first normal modes, but they  
will not be exactly the same. However, you do gain CPU time and  
memory for large systems.


My suggestion is to use the general rule for computing: don't  
optimize before you have a performance problem. If standard normal  
modes are fine for your application, stay with them.

Konrad.
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Konrad Hinsen
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