[gmx-users] Box dimension

[Mark Abraham]

Hi,

Let's be clear - so called common sense is the product of experience, and
new people should not be expected to have it. They can be expected to have
tried to solve their own problem :-) The first part of your answer looks
like it addressed your frustration, not the question. Your actual answer
included a tidbit about knowing that they act at a specific short range...

We hear that even post docs are sometimes too afraid too post here, which
is a sorry loss for everyone. I would like us all to think how to improve
ourselves a little :-)

Mark

On Mon, Jun 4, 2018, 09:34 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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