MDPOW
latest
1. Quick installation instructions for
MDPOW
2.
mdpow
— Computing the octanol/water partitioning coefficient
3. The
mdpow-*
scripts
4.
mdpow.equil
— Setting up and running equilibrium MD
5.
mdpow.fep
– Calculate free energy of solvation
6. Analysis
7. Workflows
8. Helper modules
9. Force field selection
MDPOW
Docs
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Index
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Index
Symbols
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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W
Symbols
--estimator {mdpow,alchemlyb}
mdpow-pow command line option
mdpow-solvationenergy command line option
--force
mdpow-pow command line option
mdpow-solvationenergy command line option
--ignore-corrupted
mdpow-pow command line option
mdpow-solvationenergy command line option
--method {TI,MBAR,BAR}
mdpow-pow command line option
mdpow-solvationenergy command line option
--no-SI
mdpow-pow command line option
mdpow-solvationenergy command line option
--plotfile FILE
mdpow-pow command line option
mdpow-solvationenergy command line option
--setup=<LIST>
mdpow-rebuild-fep command line option
--SI
mdpow-pow command line option
mdpow-solvationenergy command line option
--solvent NAME, -S NAME
mdpow-solvationenergy command line option
--solvent=<NAME>
mdpow-rebuild-fep command line option
mdpow-rebuild-simulation command line option
--start START
mdpow-pow command line option
mdpow-solvationenergy command line option
--stop STOP
mdpow-pow command line option
mdpow-solvationenergy command line option
-d <DIRECTORY>, --dirname=<DIRECTORY>
mdpow-equilibrium command line option
mdpow-fep command line option
-e FILE, --energies FILE
mdpow-pow command line option
mdpow-solvationenergy command line option
-h, --help
mdpow-check command line option
mdpow-equilibrium command line option
mdpow-fep command line option
mdpow-pow command line option
mdpow-rebuild-fep command line option
mdpow-rebuild-simulation command line option
mdpow-solvationenergy command line option
-o <FILE>, --outfile=<FILE>
mdpow-check command line option
-o FILE, --outfile FILE
mdpow-pow command line option
mdpow-solvationenergy command line option
-S <NAME>, --solvent=<NAME>
mdpow-equilibrium command line option
mdpow-fep command line option
-s N, --stride N
mdpow-pow command line option
mdpow-solvationenergy command line option
_
__version__ (in module mdpow)
_build_ensemble() (mdpow.analysis.ensemble.Ensemble method)
_conclude_ensemble() (mdpow.analysis.ensemble.EnsembleAnalysis method)
_conclude_universe() (mdpow.analysis.ensemble.EnsembleAnalysis method)
_generate_template_dict() (in module mdpow.config)
_load_universe_from_dir() (mdpow.analysis.ensemble.Ensemble static method)
_prepare_ensemble() (mdpow.analysis.ensemble.EnsembleAnalysis method)
_prepare_universe() (mdpow.analysis.ensemble.EnsembleAnalysis method)
_single_frame() (mdpow.analysis.ensemble.EnsembleAnalysis method)
_single_universe() (mdpow.analysis.ensemble.EnsembleAnalysis method)
A
add_system() (mdpow.analysis.ensemble.Ensemble method)
analyze() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
analyze_alchemlyb() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
arraylabel() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
automated_dihedral_analysis() (in module mdpow.workflows.dihedrals)
automated_project_analysis() (in module mdpow.workflows.base)
B
build_svg() (in module mdpow.workflows.dihedrals)
build_universe() (in module mdpow.workflows.dihedrals)
C
check_groups_from_common_ensemble() (mdpow.analysis.ensemble.EnsembleAnalysis static method)
checkpoint() (in module mdpow.restart)
clear() (mdpow.restart.Journal method)
collect() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
collect_alchemlyb() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
completed() (mdpow.restart.Journal method)
compress_dgdl_xvg() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
contains_corrupted_xvgs() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
convert_edr() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
coordinate_structures (mdpow.equil.Simulation attribute)
current (mdpow.restart.Journal attribute)
D
DEFAULT_FORCEFIELD (in module mdpow.forcefields)
defaults (in module mdpow.config)
dgdl_edr() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
dgdl_total_edr() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
dgdl_tpr() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
dgdl_xvg() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
dihedral_groups_ensemble() (in module mdpow.workflows.dihedrals)
dihedral_violins() (in module mdpow.workflows.dihedrals)
DihedralAnalysis (class in mdpow.analysis.dihedral)
DIRECTORY [DIRECTORY ...]
mdpow-pow command line option
mdpow-solvationenergy command line option
DIST (in module mdpow.equil)
E
energy_minimize() (mdpow.equil.Simulation method)
Ensemble (class in mdpow.analysis.ensemble)
ensemble (mdpow.analysis.ensemble.EnsembleAtomGroup attribute)
EnsembleAnalysis (class in mdpow.analysis.ensemble)
EnsembleAtomGroup (class in mdpow.analysis.ensemble)
environment variable
GMXLIB
,
[1]
,
[2]
,
[3]
,
[4]
PATH
equilibrium_simulation() (in module mdpow.run)
estimators (mdpow.fep.Gsolv attribute)
F
fep_dirs() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
fep_simulation() (in module mdpow.run)
FEPschedule (class in mdpow.fep)
ff_paths (mdpow.forcefields.Forcefield attribute)
filekeys (mdpow.equil.Simulation attribute)
Forcefield (class in mdpow.forcefields)
frombase() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
G
Gcyclo (class in mdpow.fep)
Gcyclo.dummy_protocol() (in module mdpow.fep)
get_atom_indices() (in module mdpow.workflows.dihedrals)
get_bond_indices() (in module mdpow.workflows.dihedrals)
get_configuration() (in module mdpow.config)
get_dihedral_groups() (in module mdpow.workflows.dihedrals)
get_last_checkpoint() (mdpow.equil.Simulation method)
get_last_structure() (mdpow.equil.Simulation method)
get_mdp_files() (in module mdpow.run)
get_paired_indices() (in module mdpow.workflows.dihedrals)
get_protocol() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
(mdpow.restart.Journalled method)
get_solvent_identifier() (in module mdpow.forcefields)
get_solvent_model() (in module mdpow.forcefields)
get_template() (in module mdpow.config)
get_templates() (in module mdpow.config)
get_water_model() (in module mdpow.forcefields)
Ghyd (class in mdpow.fep)
Ghyd.dummy_protocol() (in module mdpow.fep)
GMXLIB
,
[1]
,
[2]
,
[3]
,
[4]
Goct (class in mdpow.fep)
Goct.dummy_protocol() (in module mdpow.fep)
GROMACS_SOLVENT_MODELS (in module mdpow.forcefields)
GROMACS_WATER_MODELS (in module mdpow.forcefields)
GromacsSolventModel (class in mdpow.forcefields)
Gsolv (class in mdpow.fep)
Gsolv.dummy_protocol() (in module mdpow.fep)
Gtol (class in mdpow.fep)
Gtol.dummy_protocol() (in module mdpow.fep)
guess_elements() (in module mdpow.workflows.base)
guess_filename() (mdpow.forcefields.GromacsSolventModel method)
H
has_completed() (mdpow.restart.Journal method)
has_dVdl() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
has_not_completed() (mdpow.restart.Journal method)
history (mdpow.restart.Journal attribute)
I
includedir (in module mdpow.config)
incomplete (mdpow.restart.Journal attribute)
INTERACTIONS_DEFAULT (in module mdpow.workflows.dihedrals)
J
Journal (class in mdpow.restart)
Journalled (class in mdpow.restart)
Journalled.dummy_protocol() (in module mdpow.restart)
JournalSequenceError
K
kBOLTZ (in module mdpow.fep)
kcal_to_kJ() (in module mdpow.fep)
keys() (mdpow.analysis.ensemble.Ensemble method)
(mdpow.analysis.ensemble.EnsembleAtomGroup method)
kJ_to_kcal() (in module mdpow.fep)
L
label() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
load() (mdpow.equil.Simulation method)
(mdpow.fep.FEPschedule static method)
(mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
(mdpow.restart.Journalled method)
logger_DeltaA0() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
M
make_paths_relative() (mdpow.equil.Simulation method)
MD() (mdpow.equil.Simulation method)
MD_NPT() (mdpow.equil.Simulation method)
MD_relaxed() (mdpow.equil.Simulation method)
MD_restrained() (mdpow.equil.Simulation method)
mdp_default (mdpow.fep.Gsolv attribute)
mdp_defaults (mdpow.equil.Simulation attribute)
mdp_dict (mdpow.fep.FEPschedule attribute)
mdpow-check command line option
-h, --help
-o <FILE>, --outfile=<FILE>
mdpow-equilibrium command line option
-S <NAME>, --solvent=<NAME>
-d <DIRECTORY>, --dirname=<DIRECTORY>
-h, --help
RUNFILE
mdpow-fep command line option
-S <NAME>, --solvent=<NAME>
-d <DIRECTORY>, --dirname=<DIRECTORY>
-h, --help
RUNFILE
mdpow-pow command line option
--SI
--estimator {mdpow,alchemlyb}
--force
--ignore-corrupted
--method {TI,MBAR,BAR}
--no-SI
--plotfile FILE
--start START
--stop STOP
-e FILE, --energies FILE
-h, --help
-o FILE, --outfile FILE
-s N, --stride N
DIRECTORY [DIRECTORY ...]
mdpow-rebuild-fep command line option
--setup=<LIST>
--solvent=<NAME>
-h, --help
mdpow-rebuild-simulation command line option
--solvent=<NAME>
-h, --help
mdpow-solvationenergy command line option
--SI
--estimator {mdpow,alchemlyb}
--force
--ignore-corrupted
--method {TI,MBAR,BAR}
--no-SI
--plotfile FILE
--solvent NAME, -S NAME
--start START
--stop STOP
-e FILE, --energies FILE
-h, --help
-o FILE, --outfile FILE
-s N, --stride N
DIRECTORY [DIRECTORY ...]
mdpow.config (module)
mdpow.equil (module)
mdpow.fep (module)
mdpow.forcefields (module)
mdpow.log (module)
mdpow.restart (module)
mdpow.run (module)
mdpow.workflows.base (module)
mdpow.workflows.dihedrals (module)
mdpow.workflows.registry (module)
molar_to_nm3() (in module mdpow.fep)
N
N_AVOGADRO (in module mdpow.fep)
NoOptionWarning (class in mdpow.config)
NoSectionError
O
OctanolSimulation (class in mdpow.equil)
P
PATH
pCW() (in module mdpow.fep)
periodic_angle_padding() (in module mdpow.workflows.dihedrals)
plot() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
plot_dihedral_violins() (in module mdpow.workflows.dihedrals)
PLOT_WIDTH_DEFAULT (in module mdpow.workflows.dihedrals)
pop() (mdpow.analysis.ensemble.Ensemble method)
positions() (mdpow.analysis.ensemble.EnsembleAtomGroup method)
pOW() (in module mdpow.fep)
processed_topology() (mdpow.equil.Simulation method)
project_paths() (in module mdpow.workflows.base)
protocols (mdpow.equil.Simulation attribute)
(mdpow.fep.Gsolv attribute)
(mdpow.restart.Journalled attribute)
pTW() (in module mdpow.fep)
Q
qsub() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
R
rdkit_conversion() (in module mdpow.workflows.dihedrals)
registry (in module mdpow.workflows.registry)
results (mdpow.fep.Gsolv attribute)
run() (mdpow.analysis.dihedral.DihedralAnalysis method)
(mdpow.analysis.ensemble.EnsembleAnalysis method)
(mdpow.analysis.solvation.SolvationAnalysis method)
RUNFILE
mdpow-equilibrium command line option
mdpow-fep command line option
runMD_or_exit() (in module mdpow.run)
S
save() (mdpow.equil.Simulation method)
(mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
(mdpow.restart.Journalled method)
save_df() (in module mdpow.workflows.dihedrals)
scripts (mdpow.fep.Gsolv attribute)
select_atoms() (mdpow.analysis.ensemble.Ensemble method)
(mdpow.analysis.ensemble.EnsembleAtomGroup method)
select_systems() (mdpow.analysis.ensemble.Ensemble method)
setup() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
setupMD() (in module mdpow.run)
Simulation (class in mdpow.equil)
SMARTS_DEFAULT (in module mdpow.workflows.dihedrals)
solvate() (mdpow.equil.Simulation method)
SolvationAnalysis (class in mdpow.analysis.solvation)
SOLVENTS_DEFAULT (in module mdpow.workflows.dihedrals)
SPECIAL_WATER_COORDINATE_FILES (in module mdpow.forcefields)
start() (mdpow.restart.Journal method)
summary() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
T
tasklabel() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
templates (in module mdpow.config)
topfiles (in module mdpow.config)
topology() (mdpow.equil.Simulation method)
W
WaterSimulation (class in mdpow.equil)
wdir() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
wname() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
write_DeltaA0() (mdpow.fep.Gcyclo method)
(mdpow.fep.Ghyd method)
(mdpow.fep.Goct method)
(mdpow.fep.Gsolv method)
(mdpow.fep.Gtol method)
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