Hello,
My comments are below:
On Mon, Jan 24, 2011 at 11:15 AM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> Hi all,
>
> I am using the quasiharmonic analysis to calcualte the entropy of one
> of my molecules. First I start by aligning the whole trajectory
> including water like this
>
> center :1-20 mass origin
>
> where the first 20 residues are my peptide. Then I strip of the water
>
> strip :8-99999
>
> and last I calculate the entropy
>
> matrix mwcovar name cc.matrix out cc.matrix
> analyze matrix cc.matrix out new.matrix thermo
>
> the problem is I get a lot of warnings which I do not know how to remove
>
> ""Warning-- 161 vibrations have low frequencies and may represent hindered
> internal rotations. The contributions printed below assume that
> these
> really are vibrations.""
>
What do you mean by "remove"? There is no way to *prevent* this from being
printed (if you do, in fact, have small eigenvalues in the mass-weighted
covariance matrix) short of changing the line
if (lofreq /= 0) write(iout,1100) lofreq
in $AMBERHOME/AmberTools/ptraj/thermo.f by either commenting it out or
changing iout to 0 (stderr) and recompiling. Doing the latter will send
that message to the stderr stream, which can be separated from the output
file (and sent to /dev/null if you wish).
Hope this helps,
Jason
> Any suggestions would be very much appreciated
>
> Thanks in advance,
> Jorgen
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Jan 24 2011 - 09:00:02 PST
