Re: [AMBER] huge values for the vibrational entropy from ptraj

From: Daniel Roe <>
Date: Tue, 29 Oct 2013 09:12:40 -0600


On Tue, Oct 29, 2013 at 7:21 AM, David A Case <> 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.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Oct 29 2013 - 08:30:05 PDT
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