H2order output

User discussions
1

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

2

Hi,

“D” is Debye (dipole unit )

I guess yes, but it depends if you have specify something different

After mu_x mu_y mu_z , the average cosine with normal is printed

Best regards
Alessandra

3

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.

4

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

5

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.

6

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