Umbrella Sampling Builder
Generate umbrella windows, MDP template, and pull-code snippet.
umbrella.mdp
integrator = md nsteps = 1000000 dt = 0.002 ref_t = 300 ; Thermostat Tcoupl = v-rescale ; Barostat Pcoupl = parrinello-rahman ; Pull settings pull = yes pull_ncoords = 1 pull_coord1_type = umbrella pull_coord1_geometry = distance pull_coord1_groups = 1 2 pull_coord1_dim = Y Y Y pull_coord1_k = 1000
windows.csv
window_center_nm 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8
Pull snippet
; Example GROMACS pull settings pull = yes pull_ncoords = 1 pull_coord1_type = umbrella pull_coord1_geometry = distance pull_coord1_groups = 1 2 pull_coord1_k = 1000 pull_coord1_init = <window_center>