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!
Patch Gromacs with PLUMED.
It will be lot easier to setup enhanced sampling methods.. Umbrella Sampling, Metadynamics.. etc.
- Badges
- Science topic