[gmx-users] Calculating distance between solute and solid surface

[Ahmed Mohammed]

Hello GMX users,

I'm simulating a polymer in water on a solid surface. I'm trying to
calculate the dynamic distance between polymer monomers and the surface
(top layer of the surface). My reference is the surface and I used this
command

gmx distance -f NVT.xtc -s NVT.tpr -selrpos atom -seltype mol_com -oav
dist.xvg -tu ns

The problem is, this does not give a resonable results in comparsion
with trajectory visulization

Anyone has done same thing before that could hepe me in this?

Thank you

Ahmed