Hi,
Instead of writing out the matrix in the ‘crdaction matrix’ step, write it
out after doing ‘precision’ on the data set, eg
crdaction md-traject matrix name md-covar ...
precision md-covar 10 6
writedata covar-CA.dat md-covar
On Wed, Aug 26, 2020 at 3:57 PM Guadalupe Alvarez <gualvarez.unsam.edu.ar>
wrote:
> Dear AMBER users,
>
> I am calculating a covariance matrix with CPPTRAJ that comes with AMBER 18.
>
> It is possible that the command *precision* don't work when the *crdaction*
>
> command is used?
>
> This is my script:
>
> parm ./myparm.prmtop
>
> trajin ./mytraj.nc
>
> autoimage
>
> strip :WAT,K+,Cl-
>
> rms first :1-405.CA
>
>
>
> average crdset md-average ## Create average structure and rms fit to
>
> average
>
> createcrd md-traject ## save trajectory
>
> run
>
>
>
> crdaction md-traject rms ref md-average :1-405.CA # Fit to average
>
>
>
> crdaction md-traject matrix covar name md-covar :1-405.CA out covar-CA.dat
>
> precision covar-CA.dat 10 6
>
>
>
> The output covariance matrix I get has three decimals and I need more,
>
> because when I do the diagonalization I get more than 6 negative
>
> eigenvalues. When I don't use the *crdaction, *I get the number of decimals
>
> I ask. I can`t find an answer in the manual. Am I doing something wrong?
>
>
>
> Thanks very much!
>
> Best regards,
>
>
>
> Guadalupe.
>
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>
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>
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>
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>
>
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Received on Fri Sep 04 2020 - 11:30:02 PDT
