[MMTK] Normal Modes problem

Vasisht R. Tadigotla vasisht at eden.rutgers.edu
Wed Jun 1 18:28:15 CEST 2005


> Check what "top" says. I suspect your machine is swapping like crazy.
> On my 512 MB machine, I can't even run that job, it crashes with a
> "memory error" immediately. Yours may have more swap space, or a
> different configuration in other respects.

I have 1GB of swap, that's probably why it didn't crash with a

> For really big systems such as yours, there are two options:
> 1) Use numerical differentiation for the force constants. That's a bit
> less precise, but the derivatives are calculated only for the subspace
> basis vectors, eliminating the biggest array.
> 2) Use a sparse force constant matrix.  That's a bit slower than using
> the full one, and not supported by all force field terms, but it does
> work for the deformation force field (as well as its successor, the
> CalphaForceField) and it should be quite efficient for those
> short-ranged interactions.
> My recommendation is to try 2) first, and if that still uses too much
> memory, use 1).

I'm using the sparse matrix with the subspace modes and CalphaForceField,
and it generates the low frequency normal modes in ~10 min. Is there any
advantage in doing the full normal mode calculation with the sparse force
constant matrix, I'm only interested in the domain motions ? Would it make
a large difference in terms of the calculated B-factors ? I would also
like to estimate the frequency of motion.


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