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.