[gmx-users] gmx distance

[Teemu Murtola]

No, this does not calculate what you want. If you had an even number of K
atoms, it would even refuse to calculate. What you get is the distance
between the first and second K, third and fourth K, and so on, and finally
between the last K and the com.

You can get the individual distances with gmx pairdist (from Gromacs 5.1),
and average them yourself.

Best regards,
Teemu

On Mon, Oct 19, 2015, 00:53 Deva Priya <devapriyachem at gmail.com> wrote:

> I think I figured it out.
>
> It should be selected as "name K plus com of group XX". Running the command
> with -oall confirms that it calculates distance for each atom with name K
> and com of other group.
>
> I would still appreciate any comment, if this is a faulty solution.
>
> Thanks,
>
>
> On Sun, Oct 18, 2015 at 4:42 PM, Deva Priya <devapriyachem at gmail.com>
> wrote:
>
> > Hello,
> >
> > I am trying to set up a calculation to measure distance between the
> > following groups.
> >
> > group A = center of mass of a selection of atoms
> > group B = atoms of another group (all K atoms)
> >
> > Is it possible to specify the command such that the distance output is
> the
> > average distance between group A and each atom of group B. So, the answer
> > could be reported as average distance between all K atoms and center of
> > mass of group B.
> >
> > Any advice is greatly appreciated.
> >
> > Thanks,
> > Deva
> >
> >
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