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

[Alexander Alexander]

Thanks Mark.
I do not know what do you mean with the geometric criterion, but, It is a
slab/vacuum model in which vacuum is in the Z direction normal to the slab.
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?

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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