[gmx-users] distance from geometrical center of protein to the surface

[Wei-Ta Li]

Hello everyone,

I have run simulation of protein interacting with the infinite slab of
polymer surface and now I'm trying to calculate the distance between
protein geometrical center and the closest atom of the surface. I have read
through the manual but still don't understand how to measure such distance
with gmx tools. I have come up with the command below:

gmx distance -f protein-surface.trr -s protein-surface.tpr -n
protein-surface.ndx -oav protein-surface_dist_oav.xvg -select 'cog of group
"Protein" plus cog of group "Surface"'

However, as far as I understand it calculates distance between geometric
centers of protein and polymer slab, which is not what I am looking for. Is
there a way to select "surface" NOT "cog" for the distance measurement
between groups?

Thanks in advance!
Wei-Ta Li