Re: [AMBER] calculate entropy ptraj

From: Jason Swails <>
Date: Mon, 24 Jan 2011 11:41:41 -0500


My comments are below:

On Mon, Jan 24, 2011 at 11:15 AM, Jorgen Simonsen <>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,

> Any suggestions would be very much appreciated
> Thanks in advance,
> Jorgen
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Jan 24 2011 - 09:00:02 PST
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