[gmx-users] Box dimension

[Alex]

I will be using more smileys, I promise -- especially given how often I 
post. You know how wrong Landau was when he said: "Doing science out of 
politeness always results in complete lack of science AND politeness." A 
rude person that guy was!

By the way, those postdocs, they should check out the LAMMPS board and 
see what Axel Kohlmeyer does when you ask a question. ;)

Alex


On 6/4/2018 1:47 AM, Mark Abraham wrote:
> 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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