ok I think my question was a little more simple - how to verify that
it is okay with those low freq. values?
On Mon, Jan 24, 2011 at 5:41 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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 Tue Jan 25 2011 - 01:30:04 PST
