[gmx-users] Box dimension

[Alex]

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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