[gmx-users] Protein-Protein distance
Mark Abraham
mark.j.abraham at gmail.com
Sat Jan 30 17:00:43 CET 2016
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.inc at 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.inc at 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.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!
> >> > >>>>
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> >> > >>>>
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> >> > >>>> 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
> >> > >>
> >> > >> ==================================================
> >> > >> --
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> >> > >>
> >> > >
> >> > >
> >> > --
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