[gmx-users] gmx distance

[Teemu Murtola]

If you do not specify any other options, this will give you these minimum
distance from the com to the K atoms. If you specify the com as the -ref
selection and the K atoms as -sel, then adding -selgrouping none should
give you the 97 distances you want.

Best regards,
Teemu

On Mon, Oct 19, 2015, 12:37 Deva Priya <devapriyachem at gmail.com> wrote:

> Hello Teemu,
>
> Thanks for your response. I updated to GMX 5.1 and tried to use gmx
> pairdist.
>
> There are few examples of using pairdist correctly. So, please forgive my
> question.
>
> I tried to specify "name K" and on the second option, "com of group 13".
> This results in a distance file, which I am not sure is what I want.
>
> Do I need to specify each atom number of K with com of group 13 and then
> average the distances? or is there an easier way to do this? I have 97 K
> atoms in my simulation.
>
> Thanks again for your help.
>
> Deva
>
>
> On Mon, Oct 19, 2015 at 12:40 AM, Teemu Murtola <teemu.murtola at gmail.com>
> wrote:
>
> > 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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