# [gmx-users] Box dimension

rose rahmani rose.rhmn93 at gmail.com
Mon Jun 4 11:49:35 CEST 2018

```It's ZnS and yes it's periodic and in water not in vaccum. I used DFT just
for optimization and obtaining charges.  I did this job for an slab before.
I mean the AA was between slab surface and wall but it was the vaccum space
before slab and after wall. imagine this structures in a box of z=12. The
slab was in z=4 and wall in z=7.5 and WATER between z=4 to7.5 .... So z=0
to 4 and 7.5 to 12 is in vaccum. and AA is between z=4 to 7.5 .
I think it's clear now.

Best regards
-Rose

On Mon, 4 Jun 2018, 13:37 Alex, <nedomacho at gmail.com> wrote:

> It's a bit unclear what's happening in your system. Are you simulating
> in vacuum, or in solvent? I am assuming it's in solvent and that the
> word "vacuum" simply means space unoccupied by the structure, i.e. a
> term used by DFT folks. With all nanotubes (carbon, ZnS, BN, etc), water
> forms various interfaces at the boundary, so simply look at the
> interface data and/or other literature and see roughly how much space is
> needed to accommodate that in addition to everything else.
>
> Yes, people do put their NTs between walls with a periodic boundary,
> which requires that the nanotube edges are crystallographically
> periodic, i.e. fits a supercell. It is a very useful practice.
>
> Alex
>
>
> On 6/4/2018 2:48 AM, rose rahmani wrote:
> > Sorry i should correct myself
> >
> > On Mon, 4 Jun 2018, 13:10 rose rahmani, <rose.rhmn93 at gmail.com> wrote:
> >
> >> I have nothing to say...
> >> but i'm a beginner and i comment here to have your ideas as experienced.
> >>   It's not CNT. It's an inorganic nanotube which its partial atomic
> charges
> >> (0.48 , -0.48) is calculated by DFT.
> >>
> >> When i optimized structure in other packages i put it in box with Z=3.
> So
> >> first i have box Z=3 it means z dimension of nanotube is in z=0.85 to
> >> z=2.15 and the "COM" is in z=1.5 .
> >> So NT outer curvature which is in touch with AA is in z=2.15(0.85 + 1.3)
> >> Did you calculate these arithmetics when the z dimension of CNT started
> >> from z=0 to z=1.3?
> >>
> >> People sometimes put NT between 2 walls? As the z=7 need much more water
> >> and long calculations. Do you think put NT between two walls and use
> vaccum
> >>
> > Use box 3times distances between two walls so the vaccum is 2/3 this
> > distance
> >
> >> 3times distances between walls is better
> >>
> > than multiply 2 to keep it symmetric?(now you have 1.3 + 2*1.5 +
> thickness
> >> of two walls) how do you think, sir?
> >>
> >> With regards
> >> -Rose
> >>
> >>
> >>
> >>
> >> On 4 Jun 2018 12:04, "Alex" <nedomacho at gmail.com> wrote:
> >>
> >> I'm kind and civil, practically a sweetheart. I just can't put smiley
> >> faces everywhere! On the other hand, it does not hurt to try things and
> >> have a little bit of initiative. I don't know why I am telling you this,
> >> like you've never supervised students... Also, CNTs are simulated
> >> exactly the same way (within these forcefield flavors) as pretty much
> >> anything else you can think of. That is, until one day when you guys
> >> decide to come with a testing Gromacs version that includes FFs not
> >> relying on permanent topologies. ;)
> >>
> >>
> >> Alex
> >>
> >>
> >>
> >> On 6/4/2018 1:28 AM, Mark Abraham wrote:
> >>> 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
> >>>> --
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