Re: [gmx-users] Bash scripting and Gromacs

[Mark Abraham]

Or since you have a highly predictable sequence of integers, use a loop
over them! Bash built in printf can also be useful here. Stackoverflow.com
is a good friend for recipes.

Mark

On Tue, 26 Apr 2016 17:52 Fabricio Cannini  wrote:

> On 26-04-2016 10:33, James Starlight 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
> >
> > Thanks!
>
> Brace expansion can be useful in such cases too:
> http://www.thegeekstuff.com/2010/06/bash-shell-brace-expansion/
>
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Re: [gmx-users] Bash scripting and Gromacs

[Fabricio Cannini]

On 26-04-2016 10:33, James Starlight 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

Thanks!


Brace expansion can be useful in such cases too:
http://www.thegeekstuff.com/2010/06/bash-shell-brace-expansion/

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Re: [gmx-users] Bash scripting and Gromacs

[Kutzner, Carsten]

> On 26 Apr 2016, at 15:33, James Starlight  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 :
>> 
>>> On 26 Apr 2016, at 11:22, James Starlight  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 :
 
> On 26 Apr 2016, at 11:00, James Starlight  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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> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
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>>> --
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>>> 
>>> * Please search the archive at 
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>> 
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>> 
>> * Please search the archive at 
>> 

Re: [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 :
>
>> On 26 Apr 2016, at 11:22, James Starlight  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 :
>>>
 On 26 Apr 2016, at 11:00, James Starlight  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!

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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send 
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>>>
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>
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Re: [gmx-users] Bash scripting and Gromacs

[Kutzner, Carsten]

> On 26 Apr 2016, at 11:22, James Starlight  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 :
>> 
>>> On 26 Apr 2016, at 11:00, James Starlight  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
>>> 
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>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send 
>>> a mail to gmx-users-requ...@gromacs.org.
>> 
>> --
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Re: [gmx-users] Bash scripting and Gromacs

[James Starlight]

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

the same for trr

J.

2016-04-26 11:11 GMT+02:00 Kutzner, Carsten :
>
>> On 26 Apr 2016, at 11:00, James Starlight  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
>>
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
>> mail to gmx-users-requ...@gromacs.org.
>
> --
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Re: [gmx-users] Bash scripting and Gromacs

[Kutzner, Carsten]

> On 26 Apr 2016, at 11:00, James Starlight  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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