Révision c360028f examples/dockonsurf.inp
| b/examples/dockonsurf.inp | ||
|---|---|---|
| 1 | 1 |
# Sample of DockOnSurf input file. The file format must be an INI file. |
| 2 | 2 |
# Input format on http://forge.cbp.ens-lyon.fr/redmine/projects/dockonsurf/wiki |
| 3 | 3 |
|
| 4 |
[Global] # mandatory |
|
| 4 |
[Global] # mandatory
|
|
| 5 | 5 |
project_name = acetic_acid |
| 6 |
run_type = full # mandatory |
|
| 7 |
batch_q_sys = SGE # mandatory |
|
| 8 |
code = CP2K |
|
| 6 |
run_type = full # mandatory |
|
| 7 |
code = CP2K # mandatory |
|
| 8 |
batch_q_sys = SGE # mandatory |
|
| 9 |
max_jobs = 10r 7p 15rq |
|
| 9 | 10 |
subm_script = cp2k.sub |
| 10 |
relaunch_err = false |
|
| 11 |
max_jobs = 5 |
|
| 11 |
pbc_cell = (15.3822 0 0) (-7.6911 13.32138 0) (0 0 26.93789) |
|
| 12 | 12 |
special_atoms = (Fe1 Fe) (Fe2 Fe) (O1 O) |
| 13 | 13 |
|
| 14 |
[Isolated] |
|
| 15 |
isol_inp_file = tests/cp2k.inp # run_type-dependent
|
|
| 16 |
molec_file = tests/acetic.xyz # run_type-dependent
|
|
| 17 |
num_conformers = 500
|
|
| 14 |
[Isolated] # mandatory if isolated
|
|
| 15 |
isol_inp_file = tests/cp2k.inp # mandatory if isolated
|
|
| 16 |
molec_file = tests/acetic.xyz # mandatory if isolated
|
|
| 17 |
num_conformers = 2000
|
|
| 18 | 18 |
pre_opt = MMFF |
| 19 | 19 |
|
| 20 |
[Screening] |
|
| 21 |
screen_inp_file = tests/screen.inp # run_type-dependent |
|
| 22 |
surf_file = tests/hematite.xyz |
|
| 23 |
sites = 128 (135 138;141) # run_type-dependent |
|
| 24 |
molec_ctrs = 178 (185 187) # run_type-dependent |
|
| 25 |
molec_ctrs2 = 145 45 |
|
| 20 |
[Screening] # mandatory if screening |
|
| 21 |
screen_inp_file = tests/screen.inp # mandatory if screening |
|
| 22 |
surf_file = tests/hematite.xyz # mandatory if screening |
|
| 26 | 23 |
select_magns = energy MOI |
| 27 | 24 |
confs_per_magn = 2 |
| 28 |
surf_norm_vect = z |
|
| 29 |
h_donor = O |
|
| 30 |
set_angles = Euler |
|
| 25 |
sites = 130 (103 112 118) # mandatory if screening |
|
| 26 |
surf_norm_vect = auto |
|
| 27 |
adsorption_height = 2 |
|
| 28 |
set_angles = internal |
|
| 31 | 29 |
sample_points_per_angle = 4 |
| 32 |
min_coll_height = 5.2 |
|
| 33 |
max_structures = 30 |
|
| 34 |
collision_threshold = 0.9 |
|
| 30 |
surf_ctrs2 = 127 109 # Same number of centers as sites |
|
| 31 |
molec_ctrs = 178 (185 187) # mandatory if screening |
|
| 32 |
molec_ctrs2 = 145 45 # Same number of centers as molec_ctrs |
|
| 33 |
molec_ctrs3 = 10 9 29 1 1 # Same number of centers as molec_ctrs |
|
| 34 |
max_helic_angle = 120 |
|
| 35 |
h_donor = O |
|
| 36 |
h_acceptor = O1 |
|
| 37 |
min_coll_height = 7.0 |
|
| 38 |
collision_threshold = 1.2 |
|
| 39 |
max_structures = 500 |
|
| 35 | 40 |
|
| 36 |
[Refinement] |
|
| 37 |
refine_inp_file = tests/refine.inp # run_type-dependent
|
|
| 41 |
[Refinement] # mandatory if refinement
|
|
| 42 |
refine_inp_file = tests/refine.inp # mandatory if refinement
|
|
| 38 | 43 |
energy_cutoff = 1.0 |
Formats disponibles : Unified diff