[gmx-users] Protein-Protein distance

[Mark Abraham]

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
> >>
> >> ==================================================
> >> --
> >> Gromacs Users mailing list
> >>
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> >> posting!
> >>
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> >>
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> >>
> >
> >
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