# [gmx-users] peptide's COM distance to top of a slab

Mark Abraham mark.j.abraham at gmail.com
Tue Aug 2 22:50:55 CEST 2016

```Hi,

On Tue, Aug 2, 2016 at 10:47 PM Alexander Alexander <
alexanderwien2k at gmail.com> wrote:

> Thanks Mark.
> I do not know what do you mean with the geometric criterion,

You want to measure a distance. You need to identify two positions between
which to measure it. One of those might be some kind of average...

> but, It is a
> slab/vacuum model in which vacuum is in the Z direction normal to the slab.
>

So just look up some Z coordinates?

> I am just interested in vertical distance between peptide COM and top most
> atom.
>
> One more question is that how I can calculate the distance between the two
> termini of a peptide versas time?
>

You get a tool that can measure the displacement between one group and
another, and define one to be one terminus, and the other the other.

Mark

> Thanks,
> Alex
>
> On Tue, Aug 2, 2016 at 10:35 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > What's a geometric criterion that expresses "top of the slab?"
> >
> > Mark
> >
> > On Tue, Aug 2, 2016 at 10:22 PM Alexander Alexander <
> > alexanderwien2k at gmail.com> wrote:
> >
> > > Dear gromacs user,
> > >
> > > I have peptide getting adsorbed into a solid surface, I can get the
> > > distance between COM of peptide and COM of the slab by below command,
> > >
> > > gmx distance -n index.ndx -select 'com of group Other plus com of group
> > > Protein' -f noPBC.xtc -s prd.tpr -oxyz disxyz.xvg -tu ns
> > >
> > > I was wondering if a similar command is available to get the distance
> > > between peptide's COM and top of the slab?
> > >
> > > Regards,
> > > Alex
> > > --
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```