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E
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F
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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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S
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U
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W
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Symbols
$HOME
_
__call__() (gromacs.core.Command method)
_setup_MD() (in module gromacs.setup)
A
activate_subplot() (in module gromacs.utilities)
active (gromacs.fileformats.convert.Autoconverter attribute)
,
[1]
add_mdp_includes() (in module gromacs.cbook)
all_frames (gromacs.cbook.Frames attribute)
amino_acid_codes (in module gromacs.utilities)
AngleType (class in gromacs.fileformats.blocks)
anumb_to_atom() (gromacs.fileformats.blocks.Molecule method)
anyopen() (in module gromacs.utilities)
array (gromacs.fileformats.xpm.XPM attribute)
(gromacs.fileformats.xvg.XVG attribute)
array() (gromacs.qsub.QueuingSystem method)
array_flag() (gromacs.qsub.QueuingSystem method)
asiterable() (in module gromacs.utilities)
assemble_topology() (gromacs.fileformats.top.SystemToGroTop method)
Atom (class in gromacs.fileformats.blocks)
AtomType (class in gromacs.fileformats.blocks)
AttributeDict (class in gromacs.utilities)
autoconvert() (in module gromacs.utilities)
Autoconverter (class in gromacs.fileformats.convert)
Autoconverter.convert() (in module gromacs.fileformats.convert)
AutoCorrectionWarning
B
BadParameterWarning
besttype() (in module gromacs.fileformats.convert)
BondType (class in gromacs.fileformats.blocks)
break_array() (in module gromacs.fileformats.xvg)
C
cat() (in module gromacs.cbook)
center_fit() (gromacs.cbook.Transformer method)
cfg (in module gromacs.config)
check_file_exists() (gromacs.utilities.FileUtils method)
check_mdpargs() (in module gromacs.setup)
check_mdrun_success() (in module gromacs.run)
check_setup() (in module gromacs.config)
check_success() (gromacs.run.MDrunner method)
cleanup() (gromacs.cbook.Frames method)
CMapType (class in gromacs.fileformats.blocks)
col() (gromacs.fileformats.xpm.XPM method)
Collection (class in gromacs.collections)
combine() (gromacs.cbook.IndexBuilder method)
Command (class in gromacs.core)
commandline() (gromacs.core.GromacsCommand method)
(gromacs.run.MDrunner method)
communicate() (gromacs.core.PopenWithInput method)
CONC_WATER (in module gromacs.setup)
configdir (in module gromacs.config)
CONFIGNAME (in module gromacs.config)
configuration (gromacs.config.GMXConfigParser attribute)
(in module gromacs.config)
ConstraintType (class in gromacs.fileformats.blocks)
convert_aa_code() (in module gromacs.utilities)
create_portable_topology() (in module gromacs.cbook)
D
decimate() (gromacs.fileformats.xvg.XVG method)
decimate_circmean() (gromacs.fileformats.xvg.XVG method)
decimate_error() (gromacs.fileformats.xvg.XVG method)
decimate_max() (gromacs.fileformats.xvg.XVG method)
decimate_mean() (gromacs.fileformats.xvg.XVG method)
decimate_min() (gromacs.fileformats.xvg.XVG method)
decimate_percentile() (gromacs.fileformats.xvg.XVG method)
decimate_rms() (gromacs.fileformats.xvg.XVG method)
decimate_smooth() (gromacs.fileformats.xvg.XVG method)
defaults (in module gromacs.config)
delete_frames() (gromacs.cbook.Frames method)
detect_queuing_system() (in module gromacs.qsub)
DihedralType (class in gromacs.fileformats.blocks)
doc() (gromacs.environment.Flags method)
E
edit_mdp() (in module gromacs.cbook)
,
[1]
edit_txt() (in module gromacs.cbook)
em_schedule() (in module gromacs.setup)
energy_minimize() (in module gromacs.setup)
environment variable
$HOME
GMXBIN
GMXDATA
GROMACSWRAPPER_SUPPRESS_SETUP_CHECK
,
[1]
,
[2]
GW_START_LOGGING
LD_LIBRARY_PATH
PATH
,
[1]
,
[2]
,
[3]
,
[4]
error (gromacs.fileformats.xvg.XVG attribute)
errorbar() (gromacs.fileformats.xvg.XVG method)
Exclusion (class in gromacs.fileformats.blocks)
extract() (gromacs.cbook.Frames method)
F
failuremode (gromacs.core.GromacsCommand attribute)
filename() (gromacs.utilities.FileUtils method)
FileUtils (class in gromacs.utilities)
find_executables() (in module gromacs.tools)
find_first() (in module gromacs.utilities)
find_gromacs_command() (in module gromacs.run)
firstof() (in module gromacs.utilities)
fit() (gromacs.cbook.Transformer method)
Flag (class in gromacs.environment)
flag() (gromacs.qsub.QueuingSystem method)
Flags (class in gromacs.environment)
flags (in module gromacs.environment)
flagsDocs (class in gromacs.environment)
Frames (class in gromacs.cbook)
G
generate_submit_array() (in module gromacs.qsub)
generate_submit_scripts() (in module gromacs.qsub)
get() (gromacs.fileformats.ndx.NDX method)
get_configuration() (in module gromacs.config)
get_double_or_single_prec_mdrun() (in module gromacs.run)
get_lipid_vdwradii() (in module gromacs.setup)
get_ndx_groups() (in module gromacs.cbook)
get_template() (in module gromacs.config)
get_templates() (in module gromacs.config)
get_volume() (in module gromacs.cbook)
,
[1]
getLogLevel() (gromacs.config.GMXConfigParser method)
getpath() (gromacs.config.GMXConfigParser method)
gmx_resid() (gromacs.cbook.IndexBuilder method)
GMXBIN
GMXConfigParser (class in gromacs.config)
GMXDATA
gromacs (module)
gromacs.cbook (module)
gromacs.collections (module)
gromacs.config (module)
gromacs.core (module)
gromacs.environment (module)
gromacs.fileformats.blocks (module)
gromacs.fileformats.convert (module)
gromacs.fileformats.mdp (module)
gromacs.fileformats.ndx (module)
gromacs.fileformats.top (module)
gromacs.fileformats.xpm (module)
gromacs.fileformats.xvg (module)
gromacs.qsub (module)
gromacs.run (module)
gromacs.scaling (module)
gromacs.setup (module)
gromacs.tools (module)
gromacs.utilities (module)
GromacsCommand (class in gromacs.core)
GromacsCommandMultiIndex (class in gromacs.tools)
GromacsError
GromacsFailureWarning
GromacsImportWarning
GromacsToolLoadingError
GromacsValueWarning
GROMACSWRAPPER_SUPPRESS_SETUP_CHECK
,
[1]
,
[2]
grompp_qtot() (in module gromacs.cbook)
,
[1]
groups (gromacs.fileformats.ndx.NDX attribute)
GW_START_LOGGING
H
has_arrays() (gromacs.qsub.QueuingSystem method)
help() (gromacs.core.Command method)
(gromacs.core.GromacsCommand method)
I
ImproperType (class in gromacs.fileformats.blocks)
in_dir() (in module gromacs.utilities)
IndexBuilder (class in gromacs.cbook)
IndexSet (class in gromacs.fileformats.ndx)
infix_filename() (gromacs.utilities.FileUtils method)
InteractionType (class in gromacs.fileformats.blocks)
isMine() (gromacs.qsub.QueuingSystem method)
items() (gromacs.environment.Flags method)
iterable() (in module gromacs.utilities)
iteritems() (gromacs.environment.Flags method)
itervalues() (gromacs.environment.Flags method)
J
join() (gromacs.fileformats.ndx.uniqueNDX method)
K
keep_protein_only() (gromacs.cbook.Transformer method)
L
LD_LIBRARY_PATH
load_v4_tools() (in module gromacs.tools)
load_v5_tools() (in module gromacs.tools)
logfilename (in module gromacs.config)
loglevel_console (in module gromacs.config)
loglevel_file (in module gromacs.config)
LowAccuracyWarning
M
ma (gromacs.fileformats.xvg.XVG attribute)
make_main_index() (in module gromacs.setup)
make_ndx_captured() (in module gromacs.cbook)
make_valid_identifier() (in module gromacs.tools)
max (gromacs.fileformats.xvg.XVG attribute)
MD() (in module gromacs.setup)
MD_restrained() (in module gromacs.setup)
MDP (class in gromacs.fileformats.mdp)
MDrunner (class in gromacs.run)
MDrunnerDoublePrecision (class in gromacs.run)
MDrunnerMpich2Smpd (class in gromacs.run)
MDrunnerOpenMP (class in gromacs.run)
mean (gromacs.fileformats.xvg.XVG attribute)
merge_ndx() (in module gromacs.tools)
min (gromacs.fileformats.xvg.XVG attribute)
MissingDataError
MissingDataWarning
Molecule (class in gromacs.fileformats.blocks)
mpicommand() (gromacs.run.MDrunner method)
N
NDX (class in gromacs.fileformats.ndx)
ndxlist (gromacs.fileformats.ndx.NDX attribute)
NonbondedParamType (class in gromacs.fileformats.blocks)
number_pdbs() (in module gromacs.utilities)
O
openany() (in module gromacs.utilities)
outfile() (gromacs.cbook.Transformer method)
P
Param (class in gromacs.fileformats.blocks)
parse() (gromacs.fileformats.xpm.XPM method)
(gromacs.fileformats.xvg.XVG method)
parse_ndxlist() (in module gromacs.cbook)
,
[1]
ParseError
partial_tempering() (in module gromacs.scaling)
PATH
,
[1]
,
[2]
,
[3]
,
[4]
path (in module gromacs.config)
plot() (gromacs.fileformats.xvg.XVG method)
plot_coarsened() (gromacs.fileformats.xvg.XVG method)
Popen() (gromacs.core.Command method)
(gromacs.core.GromacsCommand method)
PopenWithInput (class in gromacs.core)
posthook() (gromacs.run.MDrunner method)
prehook() (gromacs.run.MDrunner method)
prop() (gromacs.environment.Flag method)
Q
qscript_template (in module gromacs.config)
qscriptdir (in module gromacs.config)
queuing_systems (in module gromacs.qsub)
QueuingSystem (class in gromacs.qsub)
R
read() (gromacs.fileformats.mdp.MDP method)
(gromacs.fileformats.ndx.NDX method)
(gromacs.fileformats.xpm.XPM method)
(gromacs.fileformats.xvg.XVG method)
realpath() (in module gromacs.utilities)
register() (gromacs.environment.Flags method)
remove_legend() (in module gromacs.utilities)
renumber_atoms() (gromacs.fileformats.blocks.Molecule method)
rmsd_backbone() (in module gromacs.cbook)
rp() (gromacs.cbook.Transformer method)
run() (gromacs.core.Command method)
(gromacs.core.GromacsCommand method)
(gromacs.run.MDrunner method)
run_check() (gromacs.run.MDrunner method)
S
scale_dihedrals() (in module gromacs.scaling)
scale_impropers() (in module gromacs.scaling)
set() (gromacs.fileformats.ndx.NDX method)
(gromacs.fileformats.xvg.XVG method)
set_correlparameters() (gromacs.fileformats.xvg.XVG method)
set_gmxrc_environment() (in module gromacs.config)
setdefault() (gromacs.environment.Flags method)
(gromacs.fileformats.ndx.NDX method)
SettleType (class in gromacs.fileformats.blocks)
setup() (in module gromacs.config)
size() (gromacs.fileformats.ndx.NDX method)
sizes (gromacs.fileformats.ndx.NDX attribute)
solvate() (in module gromacs.setup)
std (gromacs.fileformats.xvg.XVG attribute)
strip_fit() (gromacs.cbook.Transformer method)
strip_water() (gromacs.cbook.Transformer method)
System (class in gromacs.fileformats.blocks)
SystemToGroTop (class in gromacs.fileformats.top)
T
tc (gromacs.fileformats.xvg.XVG attribute)
templates (in module gromacs.config)
templatesdir (in module gromacs.config)
Timedelta (class in gromacs.utilities)
to_unicode() (in module gromacs.fileformats.convert)
tool_factory() (in module gromacs.tools)
TOP (class in gromacs.fileformats.top)
topology() (in module gromacs.setup)
transform_args() (gromacs.core.Command method)
(gromacs.core.GromacsCommand method)
Transformer (class in gromacs.cbook)
trj_compact() (in module gromacs.cbook)
trj_fitandcenter() (in module gromacs.cbook)
trj_xyfitted() (in module gromacs.cbook)
U
uncomment() (gromacs.fileformats.xpm.XPM static method)
uniqueNDX (class in gromacs.fileformats.ndx)
unlink_f() (in module gromacs.utilities)
unlink_gmx() (in module gromacs.utilities)
unlink_gmx_backups() (in module gromacs.utilities)
unquote() (gromacs.fileformats.xpm.XPM static method)
update() (gromacs.environment.Flags method)
UsageWarning
V
values() (gromacs.environment.Flags method)
vdw_lipid_atom_radii (in module gromacs.setup)
vdw_lipid_resnames (in module gromacs.setup)
VirtualSites3Type (class in gromacs.fileformats.blocks)
W
which() (in module gromacs.utilities)
withextsep() (in module gromacs.utilities)
write() (gromacs.fileformats.mdp.MDP method)
(gromacs.fileformats.ndx.NDX method)
(gromacs.fileformats.top.TOP method)
(gromacs.fileformats.xvg.XVG method)
X
XPM (class in gromacs.fileformats.xpm)
xvalues (gromacs.fileformats.xpm.XPM attribute)
XVG (class in gromacs.fileformats.xvg)
Y
yvalues (gromacs.fileformats.xpm.XPM attribute)
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