[gmx-users] Box dimension

Alex nedomacho at gmail.com
Mon Jun 4 09:07:52 CEST 2018

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.


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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