Umbrella Sampling

Umbrella Sampling

;Pull code
pull = yes
pull_ncoords = 1
pull_ngroups = 2
pull_group1_name = Chain_A
pull_group2_name = Chain_B
pull_coord1_type = umbrella
pull_coord1_geometry = distance
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = yes
pull_coord1_rate = 0.01 ;0.01 nm per ps
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
 Umbrella Sampling

𝒓  𝒄𝒐𝒎 =𝟑 .𝟓 Å 𝒓  𝒄𝒐𝒎 =𝟏𝟓 Å

Umbrella Sampling
Umbrella Sampling
Umbrella Sampling

; Pull code
pull = yes
pull_ncoords =1
pull_ngroups =2
pull_group1_name = Chain_A
pull_group2_name = Chain_B
pull_coord1_type = umbrella
pull_coord1_geometry = distance
pull_coord1_dim =NNY
pull_coord1_groups = 1 2
pull_coord1_start = yes
pull_coord1_rate = 0.0 ; restrain in plane
pull_coord1_k = 1000
Umbrella Sampling
Umbrella Sampling
Umbrella Sampling
Umbrella Sampling
Umbrella Sampling
Umbrella Sampling
Umbrella Sampling
Umbrella Sampling
Umbrella Sampling
Umbrella Sampling
Umbrella Sampling
Umbrella Sampling
Umbrella Sampling

Umbrella sampling is a technique in computational

physics and chemistry, used to improve sampling of a
system (or different systems) where ergodicity is
hindered by the form of the system's energy
landscape. It was first suggested by Torrie and Valleau
in 1977
PMF and Protein Conformations
 10 blocks of 10
Irreversible Pulling ( v = 10 Å/ns ) trajectories

PMF (kcal/mol)
winner
PMF (kcal/mol)

end-to-end distance (Å) end-to-end distance (Å)

 10 blocks of 10
Irreversible Pulling ( v = 100 Å/ns ) trajectories

PMF (kcal/mol)

winner
PMF (kcal/mol)

end-to-end distance (Å) end-to-end distance (Å)

Umbrella Sampling w/ WHAM
 Weighted Histogram Analysis Method

SMD
trajectory

Biasing potential:

Choice of Dt:
 Weighted Histogram Analysis Method
P0i(x), i = 1,2,…,M: overlapping
local distributions

P0(x): reconstructed overall

distribution

Underlying potential:
U0(x) = -kBT ln P0(x)
To reconstruct P0(x) from P0i(x) (i=1,2,…,M)

Ni = number of data points in distribution i,

Biasing potential: Us(x,t) = k(x-vt)2

NIH Resource for Macromolecular Modeling and Bioinformatics

Theoretical Biophysics Group, Beckman Institute, UIUC
 SMD-Jarzynski Umbrella Sampling
(equal amount of simulation time)

simple analysis coupled nonlinear equations (WHAM)

uniform sampling of the reaction coordinate nonuniform sampling of the reaction coordinate