Dear all,
I hope you are doing well,
I want to potential of mean force (PME) using the umbrella sampling
algorithm as one methane molecule is dragged following one straight line along the z direction
of the simulation box. My simulation box looks as follows.
How can I set umbrella sampling setting ? Could any one help me please?
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name =
pull_group2_name =
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 = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
Deme