> On 26 Apr 2016, at 11:22, James Starlight <jmsstarli...@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 <ckut...@gwdg.de>: >> >>> On 26 Apr 2016, at 11:00, James Starlight <jmsstarli...@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-requ...@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-requ...@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-requ...@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-requ...@gromacs.org.