Hi,
On Tue, Oct 29, 2013 at 7:21 AM, David A Case <case.biomaps.rutgers.edu> wrote:
> How many snapshots do you have? You need to have (significantly) more
> snapshots than degrees of freedom in your system. I guessing(?) you may have
> exactly 8000 snapshots, but something like 6353 atoms. You need more than
> 3*natom snapshots at a minimum.
Dave has the correct explanation here; if you generate your coordinate
covariance matrix from M samples you will have at most M non-zero
eigenvalues. So, for your ligand (2565 atoms X 3 coords/atom) you will
need to use at minimum 7695 frames. Using all available frames is
probably your best bet. Also, you may want to try using cpptraj; the
NetCDF trajectory read and matrix calculation routines are faster than
they are in ptraj.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Oct 29 2013 - 08:30:05 PDT
