[gmx-users] Protein-Protein distance

Life Sciences Inc contact.lifesciences.inc at gmail.com
Sat Jan 30 16:58:51 CET 2016 

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
>> > >>>>
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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
>> > >>
>> > >> ==================================================
>> > >> --
>> > >> Gromacs Users mailing list
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>> > >> posting!
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>> > >> send a mail to gmx-users-request at gromacs.org.
>> > >>
>> > >
>> > >
>> > --
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>
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