On Wed, Mar 25, 2015 at 5:42 AM, Vijay Achari <glycoamber.gmail.com> wrote:
> Is that possible to run the for command from cpptraj command?
One glance at the manual will show that it is not so.
> Or is that any other way to do the calculation by reading the TRAJECTORY
> only once and do the repeated calculation iteratively?
Why not use a script to create your input, then run cpptraj? E.g.
cat > input <<EOF
parm ../../../../only-nc-Format-bcmLyo25perR/bcmLyo25perR.prmtop
trajin ../../../../only-nc-Format-bcmLyo25perR/md-all-bcmLyo25perR.nc
15000 60000
EOF
for ((res=1; res < 129; res++)) ; do
echo "vector v1 :$res.C11 :$res.C14" >> input
done
cpptraj -i input
-Dan
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> Below I have given both the SCRIPT(I) and SCRIPT(II).
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> #####################################################################
> # SCRIPT(I)
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> *sys="bcmLyo25perR"path="../../../../only-nc-Format-$sys"top="$sys.prmtop"for
> j in {1..128};docpptraj $path/$top << EOFtrajin
> $path/md-all-bcmLyo25perR.nc 15000 60000unwrap *vector v1 :$j.C11 :$j.C14
> timecorr vec1 v1 out head1-lipid$j-C11_C14.dat order 2 tstep 1 tcorr 25000
> norm drct ptrajformatEOF*
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> *done*################################################
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> # SCRIPT(II)
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> *sys="bcmLyo25perR"path="../../../../only-nc-Format-$sys"top="$sys.prmtop"cpptraj
> $path/$top << EOFtrajin $path/md-all-bcmLyo25perR.nc 15000 60000unwrap *for
> j in {1..128};dovector v1 :$j.C11 :$j.C14 timecorr vec1 v1 out
> head1-lipid$j-C11_C14.dat order 2 tstep 1 tcorr 25000 norm drct
> ptrajformatdoneEOF*
>
> ##############################################
>
>
> Thanks in advance.
> Vijay
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Mar 25 2015 - 07:00:03 PDT
