# H2order output **URL:** \ **Category:** User discussions\ **Created:** [March 10, 2021, 7:50am UTC](https://gromacs.bioexcel.eu/t/h2order-output/1724 "2021-03-10T07:50:54Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![yasser.almeida](https://avatars.discourse-cdn.com/v4/letter/y/76d3ee/32.png) [@yasser.almeida](https://gromacs.bioexcel.eu/u/yasser.almeida)\ **Post date:** [March 10, 2021, 7:50am UTC](https://gromacs.bioexcel.eu/t/h2order-output/1724/1 "2021-03-10T07:50:54Z")
GROMACS version: 2020.1 GROMACS modification: No Hi, I am using `gmx h2order` to calculate orientational parameters of TIP3P water molecules. In the the output .xvg file, the y axis is “mu\_x, mu\_y, mu\_z (D), cosine with normal”. “mu\_x, mu\_y, mu\_z” I suppose are the cosine with respect to each axis. What does the “D” in mu\_z means? What is the normal of the box for this command? (Z axis?). Then, what the last column means? Thanks in advance, -Yasser ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [March 11, 2021, 9:49am UTC](https://gromacs.bioexcel.eu/t/h2order-output/1724/2 "2021-03-11T09:49:38Z")
Hi, > [@yasser.almeida](#): > > What does the “D” in mu\_z means? “D” is Debye (dipole unit ) > [@yasser.almeida](#): > > What is the normal of the box for this command? (Z axis?). I guess yes, but it depends if you have specify something different > [@yasser.almeida](#): > > Then, what the last column means? After mu\_x mu\_y mu\_z , the average cosine with normal is printed Best regards Alessandra ---
**Author:** ![Yogesh](https://avatars.discourse-cdn.com/v4/letter/y/49beb7/32.png) [@Yogesh](https://gromacs.bioexcel.eu/u/Yogesh)\ **Post date:** [January 1, 2022, 11:33am UTC](https://gromacs.bioexcel.eu/t/h2order-output/1724/3 "2022-01-01T11:33:01Z")
Hi all Wish you a happy new year. I have a system of 6 nanotubes oriented vertically along z. Is it possible to compute h2order individually for each nanotube? I.e. specifying different x y coordinates in the system? Thankyou for your time. ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [January 12, 2022, 8:47am UTC](https://gromacs.bioexcel.eu/t/h2order-output/1724/4 "2022-01-12T08:47:05Z")
Hi, `gmx h2order` computes the orientation of water molecules with respect to the normal of the box. I am not sure if this is what you are interested in. kind regards Alessandra ---
**Author:** ![Yogesh](https://avatars.discourse-cdn.com/v4/letter/y/49beb7/32.png) [@Yogesh](https://gromacs.bioexcel.eu/u/Yogesh)\ **Post date:** [January 12, 2022, 9:20am UTC](https://gromacs.bioexcel.eu/t/h2order-output/1724/5 "2022-01-12T09:20:08Z")
I do want to study that Dr. Alevilla but separately for individual nanotubes in my system. Is there any way to divide a system into subsystems? as i said I want to study orientation of water molecules through individual nanotubes aligned along z in my system. I hope i am making sense. ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [January 13, 2022, 1:45pm UTC](https://gromacs.bioexcel.eu/t/h2order-output/1724/6 "2022-01-13T13:45:52Z")
Hi, You can create groups with one nanotube and surrounding molecules using gmx select. Here the challenge that the water molecules will move around (maybe inside the nanotube the water residence is longer, but I have no experience nanotube and their exchange with water ) during the simulation. Thus each snapshot may have different different element in the index group and gmx h2order does not support dynamic index, thus you will have to process each snapshot separately. I suggest to try just on one snapshot to see if you get what you look for. \Alessandra