[gmx-users] Protein-Protein distance

Sat Jan 30 16:57:21 CET 2016

 #!/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.inc at 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.abraham at 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.inc at 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.inc at 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 <jalemkul at 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 <jalemkul at 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
> > >>>>
> > >>>> jalemkul at 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-request at 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
> > >>
> > >> jalemkul at 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-request at gromacs.org.
> > >>
> > >
> > >
> > --
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> >
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> > posting!
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