-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathcucurbit7uril-sams-dense.yaml
110 lines (88 loc) · 7.37 KB
/
cucurbit7uril-sams-dense.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
---
options:
verbose: no
resume_setup: yes
resume_simulation: yes
output_dir: sams-dense
experiments_dir: experiments
temperature: 298.15*kelvin
pressure: 1*atmosphere
constraints: HBonds
hydrogen_mass: 3 * amu
anisotropic_dispersion_cutoff: 9.0*angstroms
minimize: yes
processes_per_experiment: 1
#checkpoint_interval: 50
checkpoint_interval: 1 # to assess water coordinates
switch_phase_interval: 1000
annihilate_electrostatics: yes
annihilate_sterics: no
alchemical_pme_treatment: exact
#online_analysis_interval: 100
#online_analysis_target_error: 0.2
#online_analysis_minimum_iterations: 2000
# MCMC
# ----
mcmc_moves:
mc_and_md:
type: SequenceMove
move_list:
- type: MCDisplacementMove # Monte Carlo ligand displacement
- type: MCRotationMove # Monte Carlo ligand rotation
- type: LangevinSplittingDynamicsMove # 5 ps MD propagation with g-BAOAB
reassign_velocities: no
timestep: 4.0*femtosecond
splitting: 'V R R R O R R R V'
collision_rate: 1.0 / picosecond
n_steps: 1250
# Multistate samplers
# -------------------
samplers:
repex:
type: ReplicaExchangeSampler
mcmc_moves: mc_and_md
sams:
type: SAMSSampler
mcmc_moves: mc_and_md
state_update_scheme: global-jump
weight_update_method: optimal
flatness_threshold: 0.2
number_of_iterations: 50000
gamma0: 1.0
# Solvents
# --------
solvents:
tip3p:
nonbonded_method: PME
nonbonded_cutoff: 9*angstroms
# Experiments
# -----------
systems:
cb7-a1:
phase1_path: [testcase_input/a1/cb7-a1.prmtop, testcase_input/a1/cb7-a1.rst7]
phase2_path: [testcase_input/a1/a1.prmtop, testcase_input/a1/a1.rst7]
ligand_dsl: resname A1
solvent: tip3p
protocols:
a1-protocol:
complex:
alchemical_path:
lambda_restraints: [0.0, 0.008, 0.015, 0.023, 0.03, 0.038, 0.045, 0.053, 0.061, 0.068, 0.076, 0.083, 0.091, 0.098, 0.106, 0.114, 0.121, 0.129, 0.136, 0.144, 0.152, 0.159, 0.167, 0.174, 0.182, 0.189, 0.197, 0.205, 0.212, 0.22, 0.227, 0.235, 0.242, 0.25, 0.258, 0.265, 0.273, 0.28, 0.288, 0.295, 0.303, 0.311, 0.318, 0.326, 0.333, 0.341, 0.348, 0.356, 0.364, 0.371, 0.379, 0.386, 0.394, 0.402, 0.409, 0.417, 0.424, 0.432, 0.439, 0.447, 0.455, 0.462, 0.47, 0.477, 0.485, 0.492, 0.5, 0.508, 0.515, 0.523, 0.53, 0.538, 0.545, 0.553, 0.561, 0.568, 0.576, 0.583, 0.591, 0.598, 0.606, 0.614, 0.621, 0.629, 0.636, 0.644, 0.652, 0.659, 0.667, 0.674, 0.682, 0.689, 0.697, 0.705, 0.712, 0.72, 0.727, 0.735, 0.742, 0.75, 0.758, 0.765, 0.773, 0.78, 0.788, 0.795, 0.803, 0.811, 0.818, 0.826, 0.833, 0.841, 0.848, 0.856, 0.864, 0.871, 0.879, 0.886, 0.894, 0.902, 0.909, 0.917, 0.924, 0.932, 0.939, 0.947, 0.955, 0.962, 0.97, 0.977, 0.985, 0.992, 1.0]
lambda_electrostatics: [1.00, 0.99, 0.98, 0.97, 0.96, 0.95, 0.94, 0.93, 0.92, 0.91, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.05, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.000, 0.00, 0.000, 0.00, 0.000, 0.00, 0.000, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00]
lambda_sterics: [1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 0.99, 0.98, 0.97, 0.96, 0.95, 0.94, 0.93, 0.92, 0.91, 0.90, 0.89, 0.88, 0.87, 0.86, 0.85, 0.84, 0.83, 0.82, 0.81, 0.80, 0.79, 0.78, 0.77, 0.76, 0.75, 0.74, 0.73, 0.72, 0.71, 0.70, 0.69, 0.68, 0.67, 0.66, 0.65, 0.64, 0.63, 0.62, 0.61, 0.60, 0.59, 0.58, 0.57, 0.56, 0.55, 0.54, 0.53, 0.52, 0.51, 0.50, 0.49, 0.48, 0.47, 0.46, 0.45, 0.44, 0.43, 0.42, 0.41, 0.40, 0.39, 0.38, 0.37, 0.36, 0.35, 0.34, 0.33, 0.32, 0.31, 0.30, 0.29, 0.28, 0.27, 0.26, 0.25, 0.24, 0.23, 0.22, 0.21, 0.20, 0.19, 0.18, 0.17, 0.16, 0.15, 0.14, 0.13, 0.12, 0.11, 0.10, 0.095, 0.09, 0.085, 0.08, 0.075, 0.07, 0.065, 0.06, 0.05, 0.04, 0.03, 0.02, 0.01, 0.00]
solvent:
alchemical_path:
lambda_restraints: [0.0, 0.008, 0.015, 0.023, 0.03, 0.038, 0.045, 0.053, 0.061, 0.068, 0.076, 0.083, 0.091, 0.098, 0.106, 0.114, 0.121, 0.129, 0.136, 0.144, 0.152, 0.159, 0.167, 0.174, 0.182, 0.189, 0.197, 0.205, 0.212, 0.22, 0.227, 0.235, 0.242, 0.25, 0.258, 0.265, 0.273, 0.28, 0.288, 0.295, 0.303, 0.311, 0.318, 0.326, 0.333, 0.341, 0.348, 0.356, 0.364, 0.371, 0.379, 0.386, 0.394, 0.402, 0.409, 0.417, 0.424, 0.432, 0.439, 0.447, 0.455, 0.462, 0.47, 0.477, 0.485, 0.492, 0.5, 0.508, 0.515, 0.523, 0.53, 0.538, 0.545, 0.553, 0.561, 0.568, 0.576, 0.583, 0.591, 0.598, 0.606, 0.614, 0.621, 0.629, 0.636, 0.644, 0.652, 0.659, 0.667, 0.674, 0.682, 0.689, 0.697, 0.705, 0.712, 0.72, 0.727, 0.735, 0.742, 0.75, 0.758, 0.765, 0.773, 0.78, 0.788, 0.795, 0.803, 0.811, 0.818, 0.826, 0.833, 0.841, 0.848, 0.856, 0.864, 0.871, 0.879, 0.886, 0.894, 0.902, 0.909, 0.917, 0.924, 0.932, 0.939, 0.947, 0.955, 0.962, 0.97, 0.977, 0.985, 0.992, 1.0]
lambda_electrostatics: [1.00, 0.99, 0.98, 0.97, 0.96, 0.95, 0.94, 0.93, 0.92, 0.91, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.05, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.000, 0.00, 0.000, 0.00, 0.000, 0.00, 0.000, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00]
lambda_sterics: [1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 0.99, 0.98, 0.97, 0.96, 0.95, 0.94, 0.93, 0.92, 0.91, 0.90, 0.89, 0.88, 0.87, 0.86, 0.85, 0.84, 0.83, 0.82, 0.81, 0.80, 0.79, 0.78, 0.77, 0.76, 0.75, 0.74, 0.73, 0.72, 0.71, 0.70, 0.69, 0.68, 0.67, 0.66, 0.65, 0.64, 0.63, 0.62, 0.61, 0.60, 0.59, 0.58, 0.57, 0.56, 0.55, 0.54, 0.53, 0.52, 0.51, 0.50, 0.49, 0.48, 0.47, 0.46, 0.45, 0.44, 0.43, 0.42, 0.41, 0.40, 0.39, 0.38, 0.37, 0.36, 0.35, 0.34, 0.33, 0.32, 0.31, 0.30, 0.29, 0.28, 0.27, 0.26, 0.25, 0.24, 0.23, 0.22, 0.21, 0.20, 0.19, 0.18, 0.17, 0.16, 0.15, 0.14, 0.13, 0.12, 0.11, 0.10, 0.095, 0.09, 0.085, 0.08, 0.075, 0.07, 0.065, 0.06, 0.05, 0.04, 0.03, 0.02, 0.01, 0.00]
a1-experiment:
sampler: sams
system: cb7-a1
protocol: a1-protocol
restraint:
type: FlatBottom
restrained_receptor_atoms: resname CB7
restrained_ligand_atoms: resname A1
well_radius: 12.0*angstroms
spring_constant: 100.0*kilocalories_per_mole/angstrom**2
experiments: [a1-experiment]