[gmx-users] Box dimension

[Viveca Lindahl]

Perhaps a solution for those who don't like off-GROMACS topics, is to not
get involved in such threads? ;)

--
Viveca


On Mon, Jun 4, 2018 at 9:07 AM, 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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