[gmx-users] gmx distance

[Shrinath Kumar]

Take a look at
http://manual.gromacs.org/documentation/2018.2/onlinehelp/selections.html
to learn about the selection syntax in gromacs. There is an example in the
examples section that does precisely what you want.

"com of group 1 plus com of group 2"
This can be used with gmx distance to compute the distance between these
two COMs.

On 23 July 2018 at 16:32, Mateusz Bieniek <bieniekmat at gmail.com> wrote:

> Hi Andrew,
>
> I cannot answer your question about gmx distance but I have been using the
> MDAnalysis package for this kind of analysis. I am writing this in case you
> are proficient in python and need more flexibility. The code more or less
> would look like this:
>
> u=MDAnalysis.Universe(gro, xtc)
> g1 = u.select_atoms('...')
> g2 = u.select_atoms('...')
>
> for ts in u.trajectory:
>    print (g1.center_of_mass(), g2.center_of_mass())
>
> Best, Mat
>
>
> On Mon, Jul 23, 2018 at 4:04 PM Andrew Bostick <andrew.bostick1 at gmail.com>
> wrote:
>
> > Hi,
> >
> > I want to calculate distance between com of 2 groups (3 and 8)
> >
> > gmx_mpi distance -f md.xtc -s md.tpr -n index.ndx -oav dist.xvg
> >
> > After that:
> >
> > Available static index groups:
> >  Group  0 "System" (27599 atoms)
> >  Group  1 "Other" (716 atoms)
> >  Group  2 "MMM" (704 atoms)
> >  Group  3 "LIG" (12 atoms)
> >  Group  4 "Water" (26883 atoms)
> >  Group  5 "SOL" (26883 atoms)
> >  Group  6 "non-Water" (716 atoms)
> >  Group  7 "MMM_LIG" (716 atoms)
> >  Group  8 "MMM_com" (44 atoms)
> > Specify any number of selections for option 'select'
> > (Position pairs to calculate distances for):
> > (one per line, <enter> for status/groups, 'help' for help, Ctrl-D to end)
> > > ^C
> >
> > How to use option -select?
> >
> > Please guide me to use -select.
> >
> > Thanks
> > AB
> > --
> > 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.
>