Hi,
I want to calculate the 1- angle between slab surface plane and water molecule plane 2- angle between OH vector of water and slab plane.
How should i define OH vector, HOH plane and surface plane in GROMACS?
Best
Dear Pritam Kumar Panda
, i had read all above discussions. but to tell the truth i didn't understand well. I need a great example. i share you my challenges;1- the angle between HOH plane of water and and ZnS slab(surface) plane.
gmx gangle -f *.xtc -s *.tpr -n *.ndx -g1 plane -group1 ZnS -g2 SOL
is it true?
2- the angle between OH vector of water and surface plane
gmx gangle -f *.xtc -s *.tpr -n *.ndx -g1 plane -group1 ZnS -g2 OH
???
how should i define all OH vectors?
in system?
what -group1 and group2 refers to?
i made an index for one HW1 OW HW2 water molecule and the Zn1 Zn2 Zn3 but no output.
i really get confused what is the strategy in defining the all HOH plane and the surface plane in system?
would you please help me?
Best regards
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