#!/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.