Hi,
On Mon, Sep 30, 2013 at 11:58 AM, kirtana S <skirtana4.gmail.com> wrote:
> I get the warning as
> warning: setting vibrational entropy to zero for mode 10975 with vtemp = -258451981.
The issue here I think is that you are using 5000 frames of data, but
your mass-weighted covariance matrix is of order 16797; therefore you
will have at most 5000 non-zero eigenvalues (see
http://archive.ambermd.org/201309/0158.html for more details on this).
You either need to select less than 1667 atoms, (maybe try just using
heavy atoms, or alpha carbons only or something) or provide more than
16797 frames of data.
-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 Mon Sep 30 2013 - 12:00:03 PDT
