[gmx-users] Bash scripting and Gromacs

[James Starlight]

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

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,
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.