How make an index for gmx gangle?

09 September 2018 1 8K Report

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

Roja Rahmani

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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