[gmx-users] Box dimension

[rose rahmani]

Is there any suggestion about how can i make this system in least box size?
with periodic boundary condition in all dimensions?put NT in middle or at
z=0?

Best
-Rose

On Mon, Jun 4, 2018 at 2:19 PM, rose rahmani <rose.rhmn93 at gmail.com> wrote:

> 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?
>> >>>>>
>> >>>>> Would you please help me?
>> >>>>>
>> >>>>> Best regards
>> >>>>> -Rose
>> >>>> --
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>