[gmx-users] Bash scripting and Gromacs

[Kutzner, Carsten]

> On 26 Apr 2016, at 15:33, James Starlight <jmsstarlight at gmail.com> wrote:
> 
> No, in my case it recognize ? like a ?
> 
> in script I have
> 
> for sim in ${HOME}/${tit}* ; do
> if [[ -d $sim ]]; then
>  simulation=$(basename "$sim")
>  cd ${sim}
>  rm dd_dump_err*.pdb
>  trjconv -s md_${tit}?.tpr -f md_${tit}?.trr -o
> ${HOME}/output/${simulation}.xtc -n -pbc mol -ur compact -fit trans  <
> ${HOME}/enter.txt
> 
> and gromacs sent
> 
>  trjconv -s md_resp_complex?.tpr -f md_resp_complex?.trr -o
> /nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/output/resp_complex_conf7.xtc
> -n -pbc mol -ur compact -fit trans
> 
> 
> Is it possible specify more flexible e.g 1 of any character or 2 of
> any characters within the file name etc like REGEX syntax
http://www.tldp.org/LDP/Bash-Beginners-Guide/html/sect_04_01.html

Good luck :)

Carsten


> 
> Thanks!
> 
> J.
> 
> 2016-04-26 12:45 GMT+02:00 Kutzner, Carsten <ckutzne at gwdg.de>:
>> 
>>> 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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