Hello everyone,

I'm new to gromacs and also new to umbrella sampling, so I'm following Justin's tutorial http://www.mdtutorials.com/gmx/umbrella/index.html ;

On the umbrella sampling stage, I'm not seeing WHERE the harmonic potential is being applied in the .mdp:

; Pull code pull = yes pull_ncoords = 1 ; only one reaction coordinate pull_ngroups = 2 ; two groups defining one reaction coordinate pull_group1_name = Chain_A pull_group2_name = Chain_B pull_coord1_type = umbrella ; harmonic potential pull_coord1_geometry = distance ; simple distance increase pull_coord1_dim = N N Y pull_coord1_groups = 1 2 pull_coord1_start = yes ; define initial COM distance > 0 pull_coord1_rate = 0.0 ; restrain in place pull_coord1_k = 1000 ; kJ mol^-1 nm^-2

My question: does the option "pull_coord1_k" acts as the harmonic spring keeping the system "in place" now? Or is that defined on another part of the .mdp?

Thank you!