[gmx-users] Bond distance and H bonds

[Sameer Edirisinghe]

Dear users,

I need know how to find bond distance of H and O atoms of my polymer
molecule system which contain 10 molecules in a box. I used to modify .top
file .gro file to get 10 molecules in my system and i have successfully
perform the production run.

Then, I used following commands to find the bond distances to evaluate the
H bond formation.

1) gmx make_ndx

with above command, i need to know how to split 1 group into separate
groups as all of molecules has packed in same .gro file.


2) gmx distance

with above command im confusing how to select particular atom pair to find
distance at the prompt after running command.

Appreciate any guide here.