[gmx-users] Protein-Protein distance
Mark Abraham
mark.j.abraham at gmail.com
Sat Jan 30 17:05:25 CET 2016
Yes, but (at least) you've omitted the dollar sign when you use the
variable name, so the shell does not interpolate that value.
Mark
On Sat, 30 Jan 2016 17:03 Life Sciences Inc <
contact.lifesciences.inc at gmail.com> wrote:
> Thats why I have given the whole path so that I cannot make any error and
> the path to working directory is correct.
>
> On Sat, Jan 30, 2016 at 5:00 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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!
> > > >> > >>>>
> > > >> > >>>> * Can't post? Read
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> > > >> > >>>>
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> > > >> > >>>>
> > > 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
> > > >> > >>
> > > >> > >> ==================================================
> > > >> > >> --
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