Index

A | B | C | D | E | F | G | I | L | M | N | O | P | Q | R | S | T | U | V | W

A

acc-grps
mdp option
accelerate
mdp option
adress
mdp option
adress-cg-grp-names
mdp option
adress-const-wf
mdp option
adress-ex-forcecap
mdp option
adress-ex-width
mdp option
adress-hy-width
mdp option
adress-interface-correction
mdp option
adress-reference-coords
mdp option
adress-site
mdp option
adress-tf-grp-names
mdp option
adress-type
mdp option
affinity
annealing
mdp option
annealing-npoints
mdp option
annealing-temp
mdp option
annealing-time
mdp option

B

bd-fric
mdp option
bonded-lambdas
mdp option
BUILD_TESTING
cmake option

C

cache
calc-lambda-neighbors
mdp option
CASelectrons
mdp option
CASorbitals
mdp option
cmake option
BUILD_TESTING
CPPCHECK_XML_OUTPUT
GMX_BROKEN_CALLOC
GMX_BUILD_FOR_COVERAGE
GMX_BUILD_HELP
GMX_BUILD_MANUAL
GMX_BUILD_MDRUN_ONLY
GMX_BUILD_OWN_FFTW
GMX_BUILD_SHARED_EXE
GMX_BUILD_TARBALL
GMX_BUILD_UNITTESTS
GMX_COMPACT_DOXYGEN
GMX_CXX11
GMX_CYCLE_SUBCOUNTERS
GMX_DATA_INSTALL_DIR
GMX_DEVELOPER_BUILD
GMX_DOUBLE
GMX_EXTERNAL_BLAS
GMX_EXTERNAL_BOOST
GMX_EXTERNAL_LAPACK
GMX_EXTERNAL_TNG
GMX_EXTRAE
GMX_FFT_LIBRARY
GMX_GIT_VERSION_INFO
GMX_GPU
GMX_LIB_INSTALL_DIR
GMX_LOAD_PLUGINS
GMX_MPI
GMX_OPENMP
GMX_PREFER_STATIC_LIBS
GMX_SIMD
GMX_SKIP_DEFAULT_CFLAGS
GMX_SOFTWARE_INVSQRT
GMX_THREAD_MPI
GMX_USE_RDTSCP
GMX_USE_TNG
GMX_VMD_PLUGIN_PATH
GMX_X11
GMX_XML
REGRESSIONTEST_DOWNLOAD
REGRESSIONTEST_PATH
SOURCE_MD5SUM
comm-grps
mdp option
comm-mode
mdp option
compressed-x-grps
mdp option
compressed-x-precision
mdp option
compressibility
mdp option
constraint-algorithm
mdp option
constraints
mdp option
continuation
mdp option
core
cos-acceleration
mdp option
coul-lambdas
mdp option
coulomb-modifier
mdp option
coulombtype
mdp option
couple-intramol
mdp option
couple-lambda0
mdp option
couple-lambda1
mdp option
couple-moltype
mdp option
CPPCHECK_XML_OUTPUT
cmake option
CUDA
cutoff-scheme
mdp option

D

define
mdp option
deform
mdp option
delta-lambda
mdp option
dh-hist-size
mdp option
dh-hist-spacing
mdp option
dhdl-derivatives
mdp option
dhdl-print-energy
mdp option
DispCorr
mdp option
disre
mdp option
disre-fc
mdp option
disre-mixed
mdp option
disre-tau
mdp option
disre-weighting
mdp option
Domain Decomposition
dt
mdp option

E

E-x
E-y ; E-z; mdp option
E-xt
E-yt; E-zt:; mdp option
E-y ; E-z; mdp option
E-x
E-yt; E-zt:; mdp option
E-xt
emstep
mdp option
emtol
mdp option
energygrp-excl:
mdp option
energygrp-table
mdp option
energygrps
mdp option
epsilon-r
mdp option
epsilon-rf
mdp option
epsilon-surface
mdp option
ewald-geometry
mdp option
ewald-rtol
mdp option
ewald-rtol-lj
mdp option
expanded
mdp option

F

fcstep
mdp option
fep-lambdas
mdp option
fourier-nx
mdp option
fourier-ny
mdp option
fourier-nz
mdp option
fourierspacing
mdp option
free-energy
mdp option
freezedim
mdp option
freezegrps
mdp option

G

gb-algorithm
mdp option
gb-dielectric-offset
mdp option
gb-epsilon-solvent
mdp option
gb-obc-alpha
mdp option
gb-obc-beta
mdp option
gb-obc-gamma
mdp option
gb-saltconc
mdp option
gen-seed
mdp option
gen-temp
mdp option
gen-vel
mdp option
GMX_BROKEN_CALLOC
cmake option
GMX_BUILD_FOR_COVERAGE
cmake option
GMX_BUILD_HELP
cmake option
GMX_BUILD_MANUAL
cmake option
GMX_BUILD_MDRUN_ONLY
cmake option
GMX_BUILD_OWN_FFTW
cmake option
GMX_BUILD_SHARED_EXE
cmake option
GMX_BUILD_TARBALL
cmake option
GMX_BUILD_UNITTESTS
cmake option
GMX_COMPACT_DOXYGEN
cmake option
GMX_CXX11
cmake option
GMX_CYCLE_SUBCOUNTERS
cmake option
GMX_DATA_INSTALL_DIR
cmake option
GMX_DEVELOPER_BUILD
cmake option
GMX_DOUBLE
cmake option
GMX_EXTERNAL_BLAS
cmake option
GMX_EXTERNAL_BOOST
cmake option
GMX_EXTERNAL_LAPACK
cmake option
GMX_EXTERNAL_TNG
cmake option
GMX_EXTRAE
cmake option
GMX_FFT_LIBRARY
cmake option
GMX_GIT_VERSION_INFO
cmake option
GMX_GPU
cmake option
GMX_LIB_INSTALL_DIR
cmake option
GMX_LOAD_PLUGINS
cmake option
GMX_MPI
cmake option
GMX_OPENMP
cmake option
GMX_PREFER_STATIC_LIBS
cmake option
GMX_SIMD
cmake option
GMX_SKIP_DEFAULT_CFLAGS
cmake option
GMX_SOFTWARE_INVSQRT
cmake option
GMX_THREAD_MPI
cmake option
GMX_USE_RDTSCP
cmake option
GMX_USE_TNG
cmake option
GMX_VMD_PLUGIN_PATH
cmake option
GMX_X11
cmake option
GMX_XML
cmake option
GPU

I

implicit-solvent
mdp option
include
mdp option
init-lambda
mdp option
init-lambda-state
mdp option
init-lambda-weights:
mdp option
init-step
mdp option
init-wl-delta
mdp option
integrator
mdp option

L

ld-seed
mdp option
lincs-iter
mdp option
lincs-order
mdp option
lincs-warnangle
mdp option
lj-pme-comb-rule
mdp option
lmc-forced-nstart
mdp option
lmc-gibbsdelta
mdp option
lmc-mc-move
mdp option
lmc-repeats
mdp option
lmc-seed
mdp option
lmc-stats
mdp option
lmc-weights-equil
mdp option

M

mass-lambdas
mdp option
mc-temperature
mdp option
mdp option
CASelectrons
CASorbitals
DispCorr
QMMM
QMMM-grps
QMMMscheme
QMbasis
QMcharge
QMmethod
QMmult
SH
acc-grps
accelerate
adress
adress-cg-grp-names
adress-const-wf
adress-ex-forcecap
adress-ex-width
adress-hy-width
adress-interface-correction
adress-reference-coords
adress-site
adress-tf-grp-names
adress-type
annealing
annealing-npoints
annealing-temp
annealing-time
bd-fric
bonded-lambdas
calc-lambda-neighbors
comm-grps
comm-mode
compressed-x-grps
compressed-x-precision
compressibility
constraint-algorithm
constraints
continuation
cos-acceleration
coul-lambdas
coulomb-modifier
coulombtype
couple-intramol
couple-lambda0
couple-lambda1
couple-moltype
cutoff-scheme
define
deform
delta-lambda
dh-hist-size
dh-hist-spacing
dhdl-derivatives
dhdl-print-energy
disre
disre-fc
disre-mixed
disre-tau
disre-weighting
dt
emstep
emtol
energygrp-excl:
energygrp-table
energygrps
epsilon-r
epsilon-rf
epsilon-surface
ewald-geometry
ewald-rtol
ewald-rtol-lj
expanded
fcstep
fep-lambdas
fourier-nx
fourier-ny
fourier-nz
fourierspacing
free-energy
freezedim
freezegrps
gb-algorithm
gb-dielectric-offset
gb-epsilon-solvent
gb-obc-alpha
gb-obc-beta
gb-obc-gamma
gb-saltconc
gen-seed
gen-temp
gen-vel
implicit-solvent
include
init-lambda
init-lambda-state
init-lambda-weights:
init-step
init-wl-delta
integrator
ld-seed
lincs-iter
lincs-order
lincs-warnangle
lj-pme-comb-rule
lmc-forced-nstart
lmc-gibbsdelta
lmc-mc-move
lmc-repeats
lmc-seed
lmc-stats
lmc-weights-equil
mass-lambdas
mc-temperature
mininum-var-min
morse
nbfgscorr
nh-chain-length
niter
ns-type
nst-transition-matrix
nstcalcenergy
nstcalclr
nstcgsteep
nstcomm
nstdhdl
nstdisreout
nstenergy
nsteps
nstexpanded
nstfout
nstgbradii
nstlist
nstlog
nstorireout
nstpcouple
nsttcouple
nstvout
nstxout
nstxout-compressed
nwall
orire
orire-fc
orire-fitgrp
orire-tau
pbc
pcoupl
pcoupltype
periodic-molecules
pme-order
pull
pull-constr-tol
pull-coord1-dim
pull-coord1-geometry
pull-coord1-groups
pull-coord1-init
pull-coord1-k
pull-coord1-kB
pull-coord1-origin
pull-coord1-rate
pull-coord1-start
pull-coord1-type:
pull-coord1-vec
pull-cylinder-r
pull-group1-name
pull-group1-pbcatom
pull-group1-weights
pull-ncoords
pull-ngroups
pull-nstfout
pull-nstxout
pull-print-com1
pull-print-com2
pull-print-components
pull-print-ref-value
rcoulomb
rcoulomb-switch
ref-p
ref-t
refcoord-scaling
restraint-lambdas
rgbradii
rlist
rlistlong
rtpi
rvdw
rvdw-switch
sa-algorithm
sa-surface-tension
sc-alpha
sc-coul
sc-power
sc-r-power
sc-sigma
separate-dhdl-file
shake-tol
sim-temp-high
sim-temp-low
simulated-tempering
simulated-tempering-scaling
symmetrized-transition-matrix
table
table-extension
tau-p
tau-t
tc-grps
tcoupl
temperature-lambdas
tinit
user1-grps
user2-grps
userint1 (0)
userint2 (0)
userint3 (0)
userint4 (0)
userreal1 (0)
userreal2 (0)
userreal3 (0)
userreal4 (0)
vdw-lambdas
vdw-modifier
vdwtype
verlet-buffer-tolerance
wall-atomtype
wall-density
wall-ewald-zfac
wall-r-linpot
wall-type
wl-oneovert
wl-ratio
wl-scale
mininum-var-min
mdp option
morse
mdp option
MPI

N

nbfgscorr
mdp option
nh-chain-length
mdp option
niter
mdp option
node
ns-type
mdp option
nst-transition-matrix
mdp option
nstcalcenergy
mdp option
nstcalclr
mdp option
nstcgsteep
mdp option
nstcomm
mdp option
nstdhdl
mdp option
nstdisreout
mdp option
nstenergy
mdp option
nsteps
mdp option
nstexpanded
mdp option
nstfout
mdp option
nstgbradii
mdp option
nstlist
mdp option
nstlog
mdp option
nstorireout
mdp option
nstpcouple
mdp option
nsttcouple
mdp option
nstvout
mdp option
nstxout
mdp option
nstxout-compressed
mdp option
nwall
mdp option

O

OpenMP
orire
mdp option
orire-fc
mdp option
orire-fitgrp
mdp option
orire-tau
mdp option

P

Particle-mesh Ewald
pbc
mdp option
pcoupl
mdp option
pcoupltype
mdp option
periodic-molecules
mdp option
pme-order
mdp option
pull
mdp option
pull-constr-tol
mdp option
pull-coord1-dim
mdp option
pull-coord1-geometry
mdp option
pull-coord1-groups
mdp option
pull-coord1-init
mdp option
pull-coord1-k
mdp option
pull-coord1-kB
mdp option
pull-coord1-origin
mdp option
pull-coord1-rate
mdp option
pull-coord1-start
mdp option
pull-coord1-type:
mdp option
pull-coord1-vec
mdp option
pull-cylinder-r
mdp option
pull-group1-name
mdp option
pull-group1-pbcatom
mdp option
pull-group1-weights
mdp option
pull-ncoords
mdp option
pull-ngroups
mdp option
pull-nstfout
mdp option
pull-nstxout
mdp option
pull-print-com1
mdp option
pull-print-com2
mdp option
pull-print-components
mdp option
pull-print-ref-value
mdp option

Q

QMbasis
mdp option
QMcharge
mdp option
QMmethod
mdp option
QMMM
mdp option
QMMM-grps
mdp option
QMMMscheme
mdp option
QMmult
mdp option

R

rank
rcoulomb
mdp option
rcoulomb-switch
mdp option
ref-p
mdp option
ref-t
mdp option
refcoord-scaling
mdp option
REGRESSIONTEST_DOWNLOAD
cmake option
REGRESSIONTEST_PATH
cmake option
restraint-lambdas
mdp option
rgbradii
mdp option
rlist
mdp option
rlistlong
mdp option
rtpi
mdp option
rvdw
mdp option
rvdw-switch
mdp option

S

sa-algorithm
mdp option
sa-surface-tension
mdp option
sc-alpha
mdp option
sc-coul
mdp option
sc-power
mdp option
sc-r-power
mdp option
sc-sigma
mdp option
separate-dhdl-file
mdp option
SH
mdp option
shake-tol
mdp option
sim-temp-high
mdp option
sim-temp-low
mdp option
SIMD
simulated-tempering
mdp option
simulated-tempering-scaling
mdp option
socket
SOURCE_MD5SUM
cmake option
symmetrized-transition-matrix
mdp option

T

table
mdp option
table-extension
mdp option
tau-p
mdp option
tau-t
mdp option
tc-grps
mdp option
tcoupl
mdp option
temperature-lambdas
mdp option
thread
tinit
mdp option

U

user1-grps
mdp option
user2-grps
mdp option
userint1 (0)
mdp option
userint2 (0)
mdp option
userint3 (0)
mdp option
userint4 (0)
mdp option
userreal1 (0)
mdp option
userreal2 (0)
mdp option
userreal3 (0)
mdp option
userreal4 (0)
mdp option

V

vdw-lambdas
mdp option
vdw-modifier
mdp option
vdwtype
mdp option
verlet-buffer-tolerance
mdp option

W

wall-atomtype
mdp option
wall-density
mdp option
wall-ewald-zfac
mdp option
wall-r-linpot
mdp option
wall-type
mdp option
wl-oneovert
mdp option
wl-ratio
mdp option
wl-scale
mdp option