[gmx-users] Bash scripting and Gromacs

[Kutzner, Carsten]

> On 26 Apr 2016, at 11:22, James Starlight <jmsstarlight at gmail.com> wrote:
> 
> Exactly the problem was there!
> 
> BTW how to define selection more carefully (avoiding using *) tpr and
> trr to be sure that always only 1 file is selected assuming that all
> relevant trajectories and topologies are differs only on the digit e.g
> 
> resp_complex_conf7/md_resp_complex_conf7.tpr
> resp_complex_conf7/md_resp_complex_conf6.tpr
> ..
> resp_complex_conf7/md_resp_complex_conf1.tpr
For a single-character wildcard you can use a '?',
e.g.

> resp_complex_conf7/md_resp_complex_conf?.tpr


Carsten


> 
> the same for trr
> 
> J.
> 
> 2016-04-26 11:11 GMT+02:00 Kutzner, Carsten <ckutzne at gwdg.de>:
>> 
>>> 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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>> 
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