[gmx-users] Box dimension

[rose rahmani]

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
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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