-
Notifications
You must be signed in to change notification settings - Fork 0
/
west.cfg
192 lines (185 loc) · 8.42 KB
/
west.cfg
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
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
# The master WEST configuration file for a simulation.
# vi: set filetype=yaml :
---
west:
system:
module_path: $WEST_SIM_ROOT
# If you use a system driver (e.g. system.py) specify it here
# as filename.system_name
# Path to the file that contains the system
### WE Simulation options ###
# This set of options will override any setting specified in
# system driver (if set).
system_options:
# Dimensionality of your progress coordinate
pcoord_ndim: 1
# Number of data points per iteration
pcoord_len: 100
# Data type for your progress coordinate
# (can replace float32 with float64, long, int e.g. refer to numpy documentation for more details:
# http://docs.scipy.org/doc/numpy-1.10.1/user/basics.types.html)
pcoord_dtype: !!python/name:numpy.float32
# Bin settings
bins:
# There are a few bin mapping schemes available in WESTPA (refer to WESTPA wiki for more details:
# https://chong.chem.pitt.edu/wewiki/UserGuide:Constructing#Binning)
type: RectilinearBinMapper
# The bin boundary settings. Each list is for another dimension.
boundaries:
- [0,0.5, 1.0, 1.5, 2.0, 2.5, 3.0,3.5,4.0,4.5,5.0,5.1,5.2,5.3,5.4,5.5,5.6,5.7,5.8,5.9,6.0,6.1,6.2,6.3,6.4,6.5,6.6,6.7,6.8,6.9,7.0,7.1,7.2,7.3,7.4,7.5,7.6,7.7,7.8,7.9,8.0,8.1,8.2,8.3,8.4,8.5,8.6,8.7,8.8,8.9,9.0,9.1,9.2,9.3,9.4,9.5,9.6,9.7,9.8,9.9,10.0,10.5,11.0,11.5,12.0,12.5,13.0,13.5,14.0,14.5,15.0,15.5,16.0,16.5,17.0,17.5,18.0,18.5,19.0,19.5,20.0,20.5,21.0,21.5,22.0,22.5,23.0,23.50,25.0, inf]
# if there was a second dimension you are binning over it could look something like the following
# - [0.0, 0.1, 0.5, 1.0, 5.0, 10.0, 50.0, inf]
# Number walkers per bin
bin_target_counts: 504
drivers:
we_drivers: default
# There are two built in functions: 'history' and 'default'. Default is the normal WE behavior.
# History groups walkers according to their parent hist_length iterations ago.
group_function: default
#group_function: odld_system.group_walkers_test
group_arguments:
hist_length: 50
states:
# Unbound state: anything over 10 A min dist. Also, POAR RMSD isn't important.
0: [[10.0, 1.00, 0.0]]
# Bound state: anything less than 3 A min dist, and 4 A binding RMSD.
1: [[2.0, 0.1, 0.0], [2.0, 0.6, 0.0], [2.0, 1.1, 0.0], [2.0, 1.6, 0.0], [2.0, 2.1, 0.0], [2.0, 2.6, 0.0]]
propagation:
max_total_iterations: 100
max_run_wallclock: 23:00:00
propagator: executable
gen_istates: false
data:
west_data_file: west.h5
datasets: # dataset storage options
- name: pcoord # store progress coordinates with HDF5 scale/offset
dtype: float32
scaleoffset: 4 # with 4 decimal places of precision
- name: dihedral_2 # store progress coordinates with HDF5 scale/offset
dtype: float32
scaleoffset: 4 # with 4 decimal places of precision
- name: dihedral_3 # store progress coordinates with HDF5 scale/offset
dtype: float32
scaleoffset: 4 # with 4 decimal places of precision
- name: dihedral_4 # store progress coordinates with HDF5 scale/offset
dtype: float32
scaleoffset: 4 # with 4 decimal places of precision
- name: dihedral_5 # store progress coordinates with HDF5 scale/offset
dtype: float32
scaleoffset: 4 # with 4 decimal places of precision
- name: dihedral_6 # store progress coordinates with HDF5 scale/offset
dtype: float32
scaleoffset: 4 # with 4 decimal places of precision
- name: dihedral_7 # store progress coordinates with HDF5 scale/offset
dtype: float32
scaleoffset: 4 # with 4 decimal places of precision
- name: dihedral_8 # store progress coordinates with HDF5 scale/offset
dtype: float32
scaleoffset: 4 # with 4 decimal places of precision
- name: dihedral_9 # store progress coordinates with HDF5 scale/offset
dtype: float32
scaleoffset: 4 # with 4 decimal places of precision
- name: dihedral_10 # store progress coordinates with HDF5 scale/offset
dtype: float32
scaleoffset: 4 # with 4 decimal places of precision
- name: dihedral_11 # store progress coordinates with HDF5 scale/offset
dtype: float32
scaleoffset: 4 # with 4 decimal places of precision
- name: dihedral_12 # store progress coordinates with HDF5 scale/offset
dtype: float32
scaleoffset: 4 # with 4 decimal places of precision
- name: dihedral_13 # store progress coordinates with HDF5 scale/offset
dtype: float32
scaleoffset: 4 # with 4 decimal places of precision
- name: dihedral_14 # store progress coordinates with HDF5 scale/offset
dtype: float32
scaleoffset: 4 # with 4 decimal places of precision
- name: heavy_sc_rmsd_p53
dtype: float32
scaleoffset: 4 # with 4 decimal places of precision
data_refs: # how to convert segments and states to paths, etc
segment: traj_segs/{segment.n_iter:06d}/{segment.seg_id:06d}
basis_state: $WEST_SIM_ROOT/bstates/{basis_state.auxref}/P53.MDM2
initial_state: istates/{initial_state.iter_created}/{initial_state.state_id}
plugins:
- plugin: westext.wess.WESSDriver # must name Python object
enabled: false # optional, implied by presence in plugins list
do_reweighting: true
window_size: 0.5
- plugin: westext.constantratio.TargetRatio # must name Python object
enabled: true # optional, implied by presence in plugins list
max_replicas: 504
state_definitions: None
state_weights: [1]
executable:
environ: # environment variables for all executables
PROPAGATION_DEBUG: 1
datasets: # input/output for datasets
- name: heavy_sc_rmsd_p53
enabled: true # optional, implied
- name: dihedral_2
- name: dihedral_3
- name: dihedral_4
- name: dihedral_5
- name: dihedral_6
- name: dihedral_7
- name: dihedral_8
- name: dihedral_9
- name: dihedral_10
- name: dihedral_11
- name: dihedral_12
- name: dihedral_13
- name: dihedral_14
# #loader: system.coord_loader # optional, numpy.loadtxt() used by default
# stdout: pcoord.{segment.seg_id:06d}.log
# stderr: stdout
propagator:
executable: $WEST_SIM_ROOT/runseg.sh
stdout: $WEST_SIM_ROOT/seg_logs/{segment.n_iter:06d}-{segment.seg_id:06d}.log
stderr: stdout # append stderr to stdout
stdin: null # do not redirect standard input
cwd: null # do not change directory
environ: # environment variables for this executable only
SEG_DEBUG: 1
get_pcoord:
executable: $WEST_SIM_ROOT/get_pcoord.sh
stdout: pcoord.log
stderr: pcoord.err
gen_istate:
executable: $WEST_SIM_ROOT/gen_istate.sh
stdout: /dev/null
stderr: stdout
post_iteration:
enabled: false
executable: $WEST_SIM_ROOT/post_iter.sh
stdout: post_iter.log
stderr: stdout
pre_iteration:
enabled: false
executable: $WEST_SIM_ROOT/pre_iter.sh
stdout: pre_iter.log
stderr: stdout
analysis:
# Settings for w_ipa, an interactive analysis program that can also automate analysis.
directory: ANALYSIS # specify the directory all analysis files should exist in.
postanalysis: True # should the routines for w_reweight be run?
kinetics: # general options for both kinetics routines.
# Command line arguments with values should be specified as key: value (see below)
# Command line arguments that are flags without values should be included as a list value
# in the extra key (extra: [ 'disable-correl', 'disable-bootstrap' ])
# These are global options for each scheme; individual schemes can have different values,
# set in their respective section.
step_iter: 10
evolution: cumulative
extra: [ 'disable-correl' ]
analysis_schemes: # Analysis schemes. Required: name (TEST), states, and bins
TEST:
enabled: True
states:
- label: unfolded
coords: [[8.0]]
- label: folded
coords: [[1.99]]
bins:
- type: RectilinearBinMapper
boundaries: [[0.0,3.0,6.00,100000]]