[gmx-users] Box dimension

[rose rahmani]

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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