Hi,
Just to expand on Jason's answer a bit, you would e.g. generate a
pseudo-trajectory along the first PC like so:
parm complex_wt_rs.prmtop
readdata evecs.dat
runanalysis modes name evecs.dat trajout PC.1.nc trajoufmt netcdf \
trajoutmask .CA pcmin <min> pcmax <max> tmode 1
Where <min> and <max> can be chosen based on the values observed from your
'projection' command.
-Dan
On Tue, Jul 21, 2015 at 3:59 AM, antonio.coluccia.uniroma1.it <
antonio.coluccia.uniroma1.it> wrote:
> parm complex_wt_rs.prmtop
>
>
> matrix covar name matrixdat .CA out covmat.dat
>
> analyze matrix matrixdat out evecs.dat vecs 15 name myEvecs matrix
>
> analyze matrix matrixdat name evecs-ca vecs 15
>
> projection P1 modes evecs.dat out pca12.dat beg 1 end 2 @CA
>
> run
>
>
> Best regards
>
>
> Antonio
>
> --
> Antonio Coluccia, Ph.D.
> Department of Chemistry and Drugs Tecnology
> La Sapienza University
> Rome 00185
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> antonio.coluccia.uniroma1.it
> mobile: 00393406113351
>
>
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-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
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Received on Tue Jul 21 2015 - 16:30:05 PDT
