GROMACS version:2022
GROMACS modification: Yes/No
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Hi all,
How can I calculate the angle between the COG of two domains of the protein? I would like to calculate the angle change over time.
I used this command, but over time the angle is almost constant, as it shouldn’t be as I’m pulling my protein and the angle should increase.
Calculating the angle between betaI and hybrid domain :
gmx gangle -g1 angle -group1 ‘cog of group betaI plus cog of group HybridbetaI plus cog of group Hybrid’ -n …/integrindomains.ndx -f combineallnopbc3.xtc -oall angle.xvg
Thanks