[gmx-users] Problem with gmx-distance

[Teemu Murtola]

No, the atoms can be in a single group for this simple case of an atom-atom
distance.

The next line (after the prompt that you quote) should say something like
"(one per line, ..., Ctrl-D to end)". Following those instructions should
help (i.e., entering Ctrl-D).

Best regards,
Teemu

On Wed, Sep 16, 2015, 17:01 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/16/15 9:06 AM, Timofey Tyugashev wrote:
> > I want to get the distance between atoms 3770 and 5182 in my trajectory
> > After consulting with the Manual I write command:
> > gmx distance -n ind2.ndx -f trj1_WT_md_40.xtc -s wt_md.gro -oav
> distav.xvg -oall
> > dist.xvg
> > and index file ind2.ndx:
> > [ LYS_241_ODG_C1' ]
> > 3770 5182
> >
> > The program responds like this:
> >
> > Available static index groups:
> >   Group  0 "LYS_241_ODG_C1'" (2 atoms)
> > Specify any number of selections for option 'select'
> > (Position pairs to calculate distances for):
> >
> > If I pick 0, it responds 'Selection '0' parsed' and then nothing happens.
> > What to do next? The manual is incredibly murky and there are no
> examples in the
> > net.
>
> Your atoms can't be in the same group.  That was the same as with g_dist.
>
> [ atom1 ]
> 3770
> [ atom2 ]
> 5182
>
> gmx distance -n -f -s -oav -oall -select 'com of group "atom1" plus com of
> group
> "atom2"'
>
> See "gmx help selections" and specifically "gmx help selections examples"
> for
> syntax of selections and a few simple examples.
>
> -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.
>