On Wed, 26 Jan 2011 12:12:10 +0100
Jorgen Simonsen <jorgen589.gmail.com> wrote:
> Hi
>
> thanks - so I tried to rms fit using the following syntax - the
> trajectory has been centered
>
> center :1-100 mass origin
>
> rms first mass
If residues 1 to 100 are a single molecule you wouldn't need to center.
> and then do a entropy calculation
>
> matrix mwcovar name cc.matrix out cc.matrix
> analyze matrix cc.matrix out new.matrix thermo
>
> but now I start to get NaN and some very strange numbers
>
> warning: setting vibrational entropy to zero for mode 320
> with vtemp = -118786300.372960
> warning: setting vibrational entropy to zero for mode 321
> with vtemp = -4988665.26942776
Without translations and rotations included (and hence 6 degrees of
freedom removed) you should actually get six modes with frequencies
close to zero. In practice, however, I have seen similar figures as
yours. I suppose the other N - 6 modes look "fine". I am not sure
what is going on here.
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Received on Wed Jan 26 2011 - 06:00:02 PST
