[gmx-users] Protein-Protein distance

Mark Abraham mark.j.abraham at gmail.com
Sat Jan 30 17:18:22 CET 2016 

Hi,

Unfortunately we can't troubleshoot everyone's job scripts here. Go back
and consult the docs and examples for your cluster, or use a different
gromacs installation elsewhere.

Mark

On Sat, 30 Jan 2016 17:09 Life Sciences Inc <
contact.lifesciences.inc at gmail.com> wrote:

> I placed that and run the quick test the result is same no output.
>
> On Sat, Jan 30, 2016 at 5:05 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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
> > > > 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.
> > > > > >> > >>
> > > > > >> > >
> > > > > >> > >
> > > > > >> > --
> > > > > >> > 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.
> > > > > >> >
> > > > > >> --
> > > > > >> 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.
> > > > > >>
> > > > > >
> > > > > >
> > > > > --
> > > > > 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.
> > > > >
> > > > --
> > > > 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.
> > > >
> > > --
> > > 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.
> > >
> > --
> > 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.
> >
> --
> 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.
>

More information about the gromacs.org_gmx-users mailing list