# [gmx-users] Box dimension

Mark Abraham mark.j.abraham at gmail.com
Mon Jun 4 09:28:51 CEST 2018

```Hi,

Let's keep the discussion kind and civil, please. What's obvious when you
have experience often isn't when you are new. :-) I sure don't understand
the arithmetic involved, but then I've never attempted a CNT simulation!

Mark

On Mon, Jun 4, 2018, 09:08 Alex <nedomacho at gmail.com> wrote:

> And again, your question has nothing to do with Gromacs. It has to do
> with what you want to do, common sense, and basic arithmetic.
>
> CNTs interact at pretty short range (if they are intact and without edge
> passivation), so I'd just go with a distance sweep range of ~1.5 nm and
> give it some additional space, say, 1 nm, and finally keep the box
> symmetric. With CNT diameter of 1.3 nm, this would be (1.3 + 1.5 + 1) x
> 2 = 7.6 nm. You could of course place the CNT off center (in Z) to
> shorten the box.
>
> Alex
>
>
> On 6/4/2018 12:53 AM, rose rahmani wrote:
> > Hi,
> >
> > I want to do umbrella sampling for different coordination of amino acid
> > through different distances (in Z dimension) from nanotube. The nanotube
> > axis is along X axis. The COM of nanotube is in Z=1.5 and its outer
> > curvature(which is in touch with amino acid) is in Z=1.5 +0.65=2.15
> > (because the nanotube radius is 0.65nm). The initial distance of amino
> acid
> > from nanotube is 2nm. The question is how should i choose the box Z
> > dimension that some artifacts (justin explained in tutorial) doesn't
> > happen? I choose 7nm, is it ok or large?
> >
> >
> > Best regards
> > -Rose
>
> --
> 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.
>
```