How to do umbrella sampling
Contents
Gromacs
Everyone should look that Justin's tutorial first: [1]
Calculate a profile of reaction coordinates
Prepare mdp by choosing the windows
Run MD
Analyze using WHAM
cat tpr-files.dat '../output/umbrella114.tpr' cat pullf-files.dat 'pullf-umbrella114.xvg' gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
MD Inputs
Include this in mdp
; Pull code pull = yes pull_ngroups = 2 pull_ncoords = 1 pull_group1_name = Protein_&_r_918-923 pull_group2_name = Protein_&_r_396-407 pull_coord1_type = umbrella ; harmonic biasing force pull_coord1_geometry = distance ; simple distance increase pull_coord1_groups = 1 2 pull_coord1_dim = N N Y pull_coord1_rate = 0.0 pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance > 0
