Hi, Then you need to manage your working directory correctly, e.g. cd $workdir
Mark On Sat, 30 Jan 2016 16:59 Life Sciences Inc < contact.lifesciences....@gmail.com> wrote: > but when I run the command by loading the gromacs directly it runs, and > also creates output but when I submit the job through script its not > working. > > On Sat, Jan 30, 2016 at 4:57 PM, Life Sciences Inc < > contact.lifesciences....@gmail.com> wrote: > > > #!/bin/bash > > #PBS -N test > > #PBS -l ncpus=16 > > #PBS -q q02can > > #PBS -W group_list=GPU > > #PBS -l walltime=00:02:00 > > #PBS -m be > > #PBS -M contact.lifesciences....@gmail.com > > > > > > workdir="/home/Protein_Analysis/9_Assembled" > > cd workdir > > > > module load gromacs/intel/5.0.5 > > > > gmx_mpi distance -f 9_complete_pbc.xtc -s nvt.gro -n proteins_9.ndx > > -select 'com of group "protein1" plus com of group "protein2"' -oav > > 9_dist1-2 -tu ns >& 9_out1-2 & > > gmx_mpi distance -f 9_complete_pbc.xtc -s nvt.gro -n proteins_9.ndx > > -select 'com of group "protein1" plus com of group "protein3"' -oav > > 9_dist1-3 -tu ns >& 9_out1-3 & > > gmx_mpi distance -f 9_complete_pbc.xtc -s nvt.gro -n proteins_9.ndx > > -select 'com of group "protein1" plus com of group "protein4"' -oav > > 9_dist1-4 -tu ns >& 9_out1-4 & > > gmx_mpi distance -f 9_complete_pbc.xtc -s nvt.gro -n proteins_9.ndx > > -select 'com of group "protein2" plus com of group "protein3"' -oav > > 9_dist2-3 -tu ns >& 9_out2-3 & > > gmx_mpi distance -f 9_complete_pbc.xtc -s nvt.gro -n proteins_9.ndx > > -select 'com of group "protein2" plus com of group "protein4"' -oav > > 9_dist2-4 -tu ns >& 9_out2-4 & > > gmx_mpi distance -f 9_complete_pbc.xtc -s nvt.gro -n proteins_9.ndx > > -select 'com of group "protein3" plus com of group "protein4"' -oav > > 9_dist3-4 -tu ns >& 9_out3-4 & > > > > > > > > The job gets submitted in to some free host by itself (I am using qsub - > I > > option ) it runs as well, but I am not seeing any output files being > > created. > > > > On Sat, Jan 30, 2016 at 4:51 PM, Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > >> Hi, > >> > >> Sounds like your Intel version of GROMACS is also compiled with MPI. > >> That's > >> normally fine. But we need more description than "not working" in order > to > >> help you identify the problem. > >> > >> Mark > >> > >> On Sat, 30 Jan 2016 16:41 Life Sciences Inc < > >> contact.lifesciences....@gmail.com> wrote: > >> > >> > I want to ask one question regarding using gmx distance in the > script, I > >> > was able to calculate distances the way you told me Justin, command > >> doesn't > >> > run with gmx distance on gromacs 5.0.5 when I load intel version of > >> > gromacs, it runs like gmx_mpi distance but when I am using this in a > >> bash > >> > script its not working. Can anyone help me with this? I need to run > >> > multiple distance commands that's why I want to make a script. > >> > > >> > Thanks > >> > > >> > On Tue, Jan 5, 2016 at 10:45 PM, Life Sciences Inc < > >> > contact.lifesciences....@gmail.com> wrote: > >> > > >> > > OK , Thanks a lot now I got it , if I feel any difficulty further I > >> will > >> > > ask. > >> > > > >> > > Thank you > >> > > > >> > > > >> > > > >> > > On Wed, Jan 6, 2016 at 2:42 AM, Justin Lemkul <jalem...@vt.edu> > >> wrote: > >> > > > >> > >> > >> > >> > >> > >> On 1/5/16 4:11 PM, Life Sciences Inc wrote: > >> > >> > >> > >>> I am little confued to use the gmx distance command specifically > >> for my > >> > >>> purpose mentioned in my question ; > >> > >>> > >> > >>> gmx distance -f file.xtc -s file.gro -n file.ndx > >> > >>> > >> > >>> for outputting the distance between protein 1 and protein 2, > >> protein 1 > >> > >>> and > >> > >>> protein 3 , protein 1 and protein 4 I will use -oav or -oxyz or > >> -oall > >> > >>> option ?and how can I calculate the distance between the proteins > >> with > >> > >>> center of mass of my selection which I am providing though index > >> file? > >> > >>> > >> > >>> > >> > >> > >> > > >> > http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0#g_dist > >> > >> > >> > >> Read the help description to see which of the available output > >> options > >> > >> you need; they all provide slightly different content. If you just > >> want > >> > >> the total distance, use -oall, for the (x,y,z) components, use > -oxyz. > >> > >> > >> > >> The actual selection string you need to pass to -select (or choose > >> > >> interactively, as would be the case for the command you have shown) > >> > depends > >> > >> on what the groups are named/numbered in the index file. > >> > >> > >> > >> If you have, e.g. groups "protein1" and "protein2": > >> > >> > >> > >> gmx distance -f file.xtc -s file.gro -n file.ndx -selet 'com of > group > >> > >> "protein1" plus com of group "protein2"' > >> > >> > >> > >> -Justin > >> > >> > >> > >> > >> > >> > >> > >>> > >> > >>> On Tue, Jan 5, 2016 at 5:35 PM, Justin Lemkul <jalem...@vt.edu> > >> wrote: > >> > >>> > >> > >>> > >> > >>>> > >> > >>>> On 1/5/16 1:18 AM, Life Sciences Inc wrote: > >> > >>>> > >> > >>>> Dear Gromacs Users > >> > >>>>> > >> > >>>>> Kindly let me know how to calculate the protein protein distance > >> as a > >> > >>>>> function of time with gromacs. I want to calculate the distance > >> based > >> > >>>>> on > >> > >>>>> the center of mass of the selection which is CA atoms. I have 4 > >> > >>>>> proteins > >> > >>>>> in > >> > >>>>> the system and want to calculate the distances as distance > between > >> > >>>>> Protein > >> > >>>>> 1 and Protein 2, then Protein 1 and Protein 3 , then Protein 1 > and > >> > >>>>> Protein > >> > >>>>> 4. > >> > >>>>> > >> > >>>>> > >> > >>>>> I used gmx mindist command but it cannot be used to calculate > >> > distance > >> > >>>>> with > >> > >>>>> center of mass, I tried gmx distance also, but do not know how > to > >> use > >> > >>>>> it > >> > >>>>> for my above mentioned purpose. > >> > >>>>> > >> > >>>>> > >> > >>>>> gmx distance is the correct command, but you haven't told us > what > >> > >>>> you've > >> > >>>> tried and why it didn't work (or why you think it didn't work), > so > >> > it's > >> > >>>> not > >> > >>>> productive for us to simply guess. > >> > >>>> > >> > >>>> -Justin > >> > >>>> > >> > >>>> -- > >> > >>>> ================================================== > >> > >>>> > >> > >>>> Justin A. Lemkul, Ph.D. > >> > >>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow > >> > >>>> > >> > >>>> Department of Pharmaceutical Sciences > >> > >>>> School of Pharmacy > >> > >>>> Health Sciences Facility II, Room 629 > >> > >>>> University of Maryland, Baltimore > >> > >>>> 20 Penn St. > >> > >>>> Baltimore, MD 21201 > >> > >>>> > >> > >>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 > >> > >>>> http://mackerell.umaryland.edu/~jalemkul > >> > >>>> > >> > >>>> ================================================== > >> > >>>> -- > >> > >>>> 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. > >> > >>>> > >> > >>>> > >> > >> -- > >> > >> ================================================== > >> > >> > >> > >> Justin A. Lemkul, Ph.D. > >> > >> Ruth L. Kirschstein NRSA Postdoctoral Fellow > >> > >> > >> > >> Department of Pharmaceutical Sciences > >> > >> School of Pharmacy > >> > >> Health Sciences Facility II, Room 629 > >> > >> University of Maryland, Baltimore > >> > >> 20 Penn St. > >> > >> Baltimore, MD 21201 > >> > >> > >> > >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 > >> > >> http://mackerell.umaryland.edu/~jalemkul > >> > >> > >> > >> ================================================== > >> > >> -- > >> > >> 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. > -- 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.