[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 <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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