Hello,
I faced with the folliwing problem:
I try to make small script which will loop several folders
corresponded to the invididual simulations and procecc each trajectory
searching them by the keyword
trr_file="md_resp_complex_conf"
#!/bin/bash
HOME="/nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster"
trr_file="md_resp_complex_conf"
tit="resp_complex"
rm -r ${HOME}/output
mkdir ${HOME}/output
source /prog/gm502/bin/GMXRC
for sim in ${HOME}/${tit}* ; do
if [[ -d $sim ]]; then
simulation=$(basename "$sim")
pushd ${sim}
rm dd_dump_err*.pdb
trjconv -s ${HOME}/ref.gro -f ${trr_file}*.trr -o
${HOME}/output/${simulation}.xtc -n
popd
fi
done
finally I ontained
trjconv -s /nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/ref.gro -f
md_resp_complex_conf7_go.trr md_resp_complex_conf7.trr -o
/nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/output/resp_complex_conf7.xtc
-n -pbc nojump -ur compact -fit trans
here you see that the problem that the trajectory is repeated twisely
after -f which is the source of the error:
-f md_resp_complex_conf7_go.trr md_resp_complex_conf7.trr
Why this issue occures? As you see in my scriopt I defined all proprly
trjconv -s ${HOME}/ref.gro -f ${trr_file}*.trr -o
${HOME}/output/${simulation}.xtc -n
Thanks!
J,
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