[gmx-users] Bash scripting and Gromacs

[Kutzner, Carsten]

> On 26 Apr 2016, at 11:00, James Starlight <jmsstarlight at gmail.com> wrote:
> 
> 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
if there are several files that match your ${trr_file}* pattern, then
bash will give you all of those. Try leaving away the * 
or delete the other .trr files in that dir to make get only
one file there.

Carsten

> ${HOME}/output/${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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