MDPOW
release-0.6.1
Quick installation instructions for
POW
mdpow
— Computing the octanol/water partitioning coefficient
The
mdpow-*
scripts
mdpow.equil
— Setting up and running equilibrium MD
mdpow.fep
– Calculate free energy of solvation
Helper modules
MDPOW
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Index
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Symbols
--force
mdpow-fep command line option
mdpow-pow command line option
--get-template
mdpow-fep command line option
--ignore-corrupted
mdpow-fep command line option
mdpow-pow command line option
--setup=<LIST>
mdpow-rebuild-fep command line option
--solvent=<NAME>
mdpow-rebuild-fep command line option
mdpow-rebuild-simulation command line option
-d <DIRECTORY>, --dirname=<DIRECTORY>
mdpow-equilibrium command line option
mdpow-fep command line option
-e <FILE>, --energies=<FILE>
mdpow-fep command line option
mdpow-pow command line option
-h, --help
mdpow-check command line option
mdpow-equilibrium command line option
mdpow-fep command line option
,
[1]
mdpow-pow command line option
mdpow-rebuild-fep command line option
mdpow-rebuild-simulation command line option
-o <FILE>, --outfile=<FILE>
mdpow-check command line option
mdpow-pow command line option
-p <FILE>, --plotfile=<FILE>
mdpow-fep command line option
mdpow-pow command line option
-s <N>, --stride=<N>
mdpow-fep command line option
-S <NAME>, --solvent=<NAME>
mdpow-equilibrium command line option
mdpow-fep command line option
,
[1]
_
_generate_template_dict() (in module mdpow.config)
A
analyze() (mdpow.fep.Gsolv method)
arraylabel() (mdpow.fep.Gsolv method)
C
checkpoint() (in module mdpow.restart)
clear() (mdpow.restart.Journal method)
collect() (mdpow.fep.Gsolv method)
completed() (mdpow.restart.Journal method)
compress_dgdl_xvg() (mdpow.fep.Gsolv method)
contains_corrupted_xvgs() (mdpow.fep.Gsolv method)
convert_edr() (mdpow.fep.Gsolv method)
current (mdpow.restart.Journal attribute)
D
defaults (in module mdpow.config)
dgdl_edr() (mdpow.fep.Gsolv method)
dgdl_tpr() (mdpow.fep.Gsolv method)
dgdl_xvg() (mdpow.fep.Gsolv method)
DIST (in module mdpow.equil)
E
energy_minimize() (mdpow.equil.Simulation method)
environment variable
GMXLIB
,
[1]
,
[2]
PATH
equilibrium_simulation() (in module mdpow.run)
F
fep_dirs() (mdpow.fep.Gsolv method)
fep_simulation() (in module mdpow.run)
FEPschedule (class in mdpow.fep)
frombase() (mdpow.fep.Gsolv method)
G
Gcyclo (class in mdpow.fep)
get_configuration() (in module mdpow.config)
get_last_checkpoint() (mdpow.equil.Simulation method)
get_last_structure() (mdpow.equil.Simulation method)
get_mdp_files() (in module mdpow.run)
get_protocol() (mdpow.restart.Journalled method)
get_template() (in module mdpow.config)
get_templates() (in module mdpow.config)
Ghyd (class in mdpow.fep)
GMXLIB
,
[1]
,
[2]
Goct (class in mdpow.fep)
Gsolv (class in mdpow.fep)
H
has_completed() (mdpow.restart.Journal method)
has_dVdl() (mdpow.fep.Gsolv method)
has_not_completed() (mdpow.restart.Journal method)
history (mdpow.restart.Journal attribute)
I
includedir (in module mdpow.config)
incomplete (mdpow.restart.Journal attribute)
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)
kJ_to_kcal() (in module mdpow.fep)
L
label() (mdpow.fep.Gsolv method)
load() (mdpow.equil.Simulation method)
(mdpow.fep.FEPschedule static method)
(mdpow.restart.Journalled method)
logger_DeltaA0() (mdpow.fep.Gsolv 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_dict (mdpow.fep.FEPschedule attribute)
mdpow (module)
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
mdpow-fep command line option
--force
--get-template
--ignore-corrupted
-S <NAME>, --solvent=<NAME>
,
[1]
-d <DIRECTORY>, --dirname=<DIRECTORY>
-e <FILE>, --energies=<FILE>
-h, --help
,
[1]
-p <FILE>, --plotfile=<FILE>
-s <N>, --stride=<N>
mdpow-pow command line option
--force
--ignore-corrupted
-e <FILE>, --energies=<FILE>
-h, --help
-o <FILE>, --outfile=<FILE>
-p <FILE>, --plotfile=<FILE>
mdpow-rebuild-fep command line option
--setup=<LIST>
--solvent=<NAME>
-h, --help
mdpow-rebuild-simulation command line option
--solvent=<NAME>
-h, --help
mdpow.config (module)
mdpow.equil (module)
mdpow.fep (module)
mdpow.log (module)
mdpow.restart (module)
mdpow.run (module)
molar_to_nm3() (in module mdpow.fep)
N
N_AVOGADRO (in module mdpow.fep)
O
OctanolSimulation (class in mdpow.equil)
P
PATH
pCW() (in module mdpow.fep)
plot() (mdpow.fep.Gsolv method)
pOW() (in module mdpow.fep)
processed_topology() (mdpow.equil.Simulation method)
Q
qsub() (mdpow.fep.Gsolv method)
R
runMD_or_exit() (in module mdpow.run)
S
save() (mdpow.equil.Simulation method)
(mdpow.restart.Journalled method)
setup() (mdpow.fep.Gsolv method)
setupMD() (in module mdpow.run)
Simulation (class in mdpow.equil)
solvate() (mdpow.equil.Simulation method)
start() (mdpow.restart.Journal method)
summary() (mdpow.fep.Gsolv method)
T
tasklabel() (mdpow.fep.Gsolv 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.Gsolv method)
wname() (mdpow.fep.Gsolv method)
write_DeltaA0() (mdpow.fep.Gsolv method)
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