Will selecting heavy atoms give me a close value for entropy.
Regards
Kirtana
On Mon, Sep 30, 2013 at 2:58 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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 - 13:00:04 PDT
