Index

Symbols

--branch make-release-build.py command line option trigger-post-merge.py command line option --dry-run make-release-build.py command line option --help make-release-build.py command line option trigger-post-merge.py command line option --local make-release-build.py command line option --no-dry-run make-release-build.py command line option --no-release make-release-build.py command line option --regtest-branch trigger-post-merge.py command line option

--regtest-commit trigger-post-merge.py command line option --release make-release-build.py command line option --server make-release-build.py command line option --ssh-key make-release-build.py command line option --token make-release-build.py command line option trigger-post-merge.py command line option --type trigger-post-merge.py command line option -h make-release-build.py command line option trigger-post-merge.py command line option

A

acc-grps mdp option accelerate mdp option add_base_stage() (in module scripted_gmx_docker_builds) add_documentation_dependencies() (in module scripted_gmx_docker_builds) add_intel_llvm_compiler_build_stage() (in module scripted_gmx_docker_builds) add_mdmodule() (gmxapi._gmxapi.Context method) add_oneapi_compiler_build_stage() (in module scripted_gmx_docker_builds) add_python_stages() (in module scripted_gmx_docker_builds) add_tsan_compiler_build_stage() (in module scripted_gmx_docker_builds) adress mdp option annealing mdp option annealing-npoints mdp option annealing-temp mdp option annealing-time mdp option api_is_at_least() (in module gmxapi.version) ApiError awh mdp option awh-nbias mdp option awh-nsamples-update mdp option awh-nstout mdp option awh-nstsample mdp option awh-potential mdp option

awh-seed mdp option awh-share-multisim mdp option awh1-dim1-coord-index mdp option awh1-dim1-coord-provider mdp option awh1-dim1-cover-diameter mdp option awh1-dim1-diffusion mdp option awh1-dim1-end mdp option awh1-dim1-force-constant mdp option awh1-dim1-start mdp option awh1-equilibrate-histogram mdp option awh1-error-init mdp option awh1-growth mdp option awh1-ndim mdp option awh1-share-group mdp option awh1-target mdp option awh1-target-beta-scaling mdp option awh1-target-cutoff mdp option awh1-user-data mdp option

B

base_image_tag() (in module scripted_gmx_docker_builds) bd-fric mdp option before_script bonded-lambdas mdp option BUILD_DIR build_stages() (in module scripted_gmx_docker_builds)

BUILD_TESTING cmake option built-in function gromacs_check_compiler() gromacs_check_double() bulk-offsetA mdp option bulk-offsetB mdp option

C

cache calc-lambda-neighbors mdp option checkpoint (gmxapi.simulation.mdrun.OutputDataProxy attribute) CI_PROJECT_NAMESPACE close() (gmxapi._gmxapi.MDSession method) CMAKE cmake option BUILD_TESTING CMAKE_INSTALL_LIBDIR GMX_BROKEN_CALLOC GMX_BUILD_FOR_COVERAGE GMX_BUILD_HELP GMX_BUILD_MANUAL GMX_BUILD_OWN_FFTW GMX_BUILD_SHARED_EXE GMX_BUILD_TARBALL GMX_BUILD_UNITTESTS GMX_CLANG_CUDA GMX_CLANG_TIDY GMX_COMPACT_DOXYGEN GMX_COMPILER_WARNINGS GMX_CUDA_CLANG_FLAGS GMX_CYCLE_SUBCOUNTERS GMX_DEVELOPER_BUILD GMX_DOUBLE GMX_ENABLE_CCACHE GMX_EXTERNAL_BLAS GMX_EXTERNAL_LAPACK GMX_EXTERNAL_TNG GMX_EXTRAE GMX_FFT_LIBRARY GMX_GIT_VERSION_INFO GMX_GPU GMX_INSTALL_DATASUBDIR GMX_INSTALL_LEGACY_API GMX_INSTALL_NBLIB_API GMX_MPI GMX_OPENMP GMX_PREFER_STATIC_LIBS GMX_SIMD GMX_SKIP_DEFAULT_CFLAGS GMX_THREAD_MPI GMX_USE_PLUGINS GMX_USE_RDTSCP GMX_USE_TNG GMX_VMD_PLUGIN_PATH GMXAPI Gromacs::gmx Gromacs::gmxapi Gromacs::libgromacs GROMACS_CXX_FLAGS GROMACS_DEFINITIONS GROMACS_DIR GROMACS_INCLUDE_DIRS GROMACS_IS_DOUBLE GROMACS_LIBRARIES GROMACS_PREFER_STATIC GROMACS_SUFFIX REGRESSIONTEST_DOWNLOAD REGRESSIONTEST_PATH SOURCE_MD5SUM

CMAKE_COMPILER_SCRIPT CMAKE_INSTALL_LIBDIR cmake option CMAKE_MPI_OPTIONS comm-grps mdp option comm-mode mdp option commandline_operation() (in module gmxapi) COMPILER_MAJOR_VERSION compressed-x-grps mdp option compressed-x-precision mdp option compressibility mdp option concatenate_lists() (in module gmxapi) config() (in module gmxapi.utility) constraint-algorithm mdp option constraints mdp option Context (class in gmxapi._gmxapi) continuation mdp option copy_tprfile() (in module gmxapi._gmxapi) core cos-acceleration mdp option coul-lambdas mdp option coulomb-modifier mdp option coulombtype mdp option coupl-steps mdp option couple-intramol mdp option couple-lambda0 mdp option couple-lambda1 mdp option couple-moltype mdp option create_context() (in module gmxapi._gmxapi) CUDA cutoff-scheme mdp option cyl0-down mdp option cyl0-r mdp option cyl0-up mdp option cyl1-down mdp option cyl1-r mdp option cyl1-up mdp option

D

DataShapeError define mdp option deform mdp option delta-lambda mdp option density-guided-simulation-active mdp option density-guided-simulation-adaptive-force-scaling mdp option density-guided-simulation-adaptive-force-scaling-time-constant mdp option density-guided-simulation-atom-spreading-weight mdp option density-guided-simulation-force-constant mdp option density-guided-simulation-gaussian-transform-spreading-range-in-multiples-of-width mdp option density-guided-simulation-gaussian-transform-spreading-width mdp option density-guided-simulation-group mdp option density-guided-simulation-normalize-densities mdp option density-guided-simulation-nst mdp option density-guided-simulation-reference-density-filename mdp option density-guided-simulation-shift-vector mdp option

density-guided-simulation-similarity-measure mdp option density-guided-simulation-transformation-matrix mdp option dh-hist-size mdp option dh-hist-spacing mdp option dhdl-derivatives mdp option dhdl-print-energy mdp option directory (gmxapi.simulation.mdrun.OutputDataProxy attribute) DispCorr mdp option disre mdp option disre-fc mdp option disre-mixed mdp option disre-tau mdp option disre-weighting mdp option Domain Decomposition DRY_RUN dt mdp option dtype (gmxapi.abc.Future property)

E

electric-field-x mdp option electric-field-y mdp option electric-field-z mdp option emstep mdp option emtol mdp option energygrp-excl mdp option energygrp-table mdp option energygrps mdp option ensemble-temperature mdp option ensemble-temperature-setting mdp option

environment variable GMX_PME_NTHREADS gmxapi_ROOT epsilon-r mdp option epsilon-rf mdp option epsilon-surface mdp option Error ewald-geometry mdp option ewald-rtol mdp option ewald-rtol-lj mdp option except Exception expanded mdp option extract() (gmxapi._gmxapi.SimulationParameters method)

F

fcstep mdp option FeatureNotAvailable FeatureNotAvailableError 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 from_tpr() (in module gmxapi._gmxapi) function_wrapper() (in module gmxapi) Future (class in gmxapi.abc)

G

gen-seed mdp option gen-temp mdp option gen-vel mdp option get_cmake_stages() (in module scripted_gmx_docker_builds) GMX_BROKEN_CALLOC cmake option GMX_BUILD_FOR_COVERAGE cmake option GMX_BUILD_HELP cmake option GMX_BUILD_MANUAL 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_CLANG_CUDA cmake option GMX_CLANG_TIDY cmake option GMX_COMPACT_DOXYGEN cmake option GMX_COMPILER_WARNINGS cmake option GMX_CUDA_CLANG_FLAGS cmake option GMX_CYCLE_SUBCOUNTERS cmake option GMX_DEVELOPER_BUILD cmake option GMX_DOUBLE cmake option GMX_ENABLE_CCACHE cmake option GMX_EXTERNAL_BLAS 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_INSTALL_DATASUBDIR cmake option GMX_INSTALL_LEGACY_API cmake option GMX_INSTALL_NBLIB_API cmake option GMX_MPI cmake option GMX_OPENMP cmake option

GMX_PIPELINE_SCHEDULE GMX_PME_NTHREADS GMX_PREFER_STATIC_LIBS cmake option GMX_SIMD cmake option GMX_SKIP_DEFAULT_CFLAGS cmake option GMX_THREAD_MPI cmake option GMX_USE_PLUGINS cmake option GMX_USE_RDTSCP cmake option GMX_USE_TNG cmake option GMX_VMD_PLUGIN_PATH cmake option GMXAPI cmake option gmxapi module gmxapi._gmxapi module gmxapi._logging module gmxapi.exceptions module gmxapi.simulation module gmxapi.utility module gmxapi.version module gmxapi_ROOT GPU Gromacs::gmx cmake option Gromacs::gmxapi cmake option Gromacs::libgromacs cmake option gromacs_check_compiler() built-in function gromacs_check_double() built-in function GROMACS_CXX_FLAGS cmake option GROMACS_DEFINITIONS cmake option GROMACS_DIR cmake option GROMACS_INCLUDE_DIRS cmake option GROMACS_IS_DOUBLE cmake option GROMACS_LIBRARIES cmake option GROMACS_MAJOR_VERSION GROMACS_PREFER_STATIC cmake option GROMACS_RELEASE GROMACS_SUFFIX cmake option

H

has_feature() (in module gmxapi._gmxapi) (in module gmxapi.version)

hpccm_distro_name() (in module scripted_gmx_docker_builds)

I

image image_name() (in module utility) 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 iontype0-in-A mdp option iontype0-in-B mdp option iontype0-name mdp option iontypes mdp option

J

job cache

join_arrays() (in module gmxapi) join_path() (in module gmxapi.utility)

L

launch() (gmxapi._gmxapi.MDSystem method) 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 logical_not() (in module gmxapi)

M

make-release-build.py command line option --branch --dry-run --help --local --no-dry-run --no-release --release --server --ssh-key --token -h make_constant() (in module gmxapi) mass-lambdas mdp option massw-split0 mdp option massw-split1 mdp option mc-temperature mdp option MDArgs (class in gmxapi._gmxapi) mdp option acc-grps accelerate adress annealing annealing-npoints annealing-temp annealing-time awh awh-nbias awh-nsamples-update awh-nstout awh-nstsample awh-potential awh-seed awh-share-multisim awh1-dim1-coord-index awh1-dim1-coord-provider awh1-dim1-cover-diameter awh1-dim1-diffusion awh1-dim1-end awh1-dim1-force-constant awh1-dim1-start awh1-equilibrate-histogram awh1-error-init awh1-growth awh1-ndim awh1-share-group awh1-target awh1-target-beta-scaling awh1-target-cutoff awh1-user-data bd-fric bonded-lambdas bulk-offsetA bulk-offsetB 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 coupl-steps couple-intramol couple-lambda0 couple-lambda1 couple-moltype cutoff-scheme cyl0-down cyl0-r cyl0-up cyl1-down cyl1-r cyl1-up define deform delta-lambda density-guided-simulation-active density-guided-simulation-adaptive-force-scaling density-guided-simulation-adaptive-force-scaling-time-constant density-guided-simulation-atom-spreading-weight density-guided-simulation-force-constant density-guided-simulation-gaussian-transform-spreading-range-in-multiples-of-width density-guided-simulation-gaussian-transform-spreading-width density-guided-simulation-group density-guided-simulation-normalize-densities density-guided-simulation-nst density-guided-simulation-reference-density-filename density-guided-simulation-shift-vector density-guided-simulation-similarity-measure density-guided-simulation-transformation-matrix dh-hist-size dh-hist-spacing dhdl-derivatives dhdl-print-energy DispCorr disre disre-fc disre-mixed disre-tau disre-weighting dt electric-field-x electric-field-y electric-field-z emstep emtol energygrp-excl energygrp-table energygrps ensemble-temperature ensemble-temperature-setting 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 gen-seed gen-temp gen-vel implicit-solvent include init-lambda init-lambda-state init-lambda-weights init-step init-wl-delta integrator iontype0-in-A iontype0-in-B iontype0-name iontypes 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 massw-split0 massw-split1 mc-temperature mininum-var-min morse mts mts-level2-factor mts-level2-forces mts-levels nbfgscorr nh-chain-length niter nst-transition-matrix nstcalcenergy nstcgsteep nstcomm nstdhdl nstdisreout nstenergy nsteps nstexpanded nstfout nstlist nstlog nstorireout nstpcouple nsttcouple nstvout nstxout nstxout-compressed nwall orire orire-fc orire-fitgrp orire-tau pbc pcoupl pcoupltype periodic-molecules pme-order print-nose-hoover-chain-variables pull pull-constr-tol pull-coord1-dim pull-coord1-dx pull-coord1-expression pull-coord1-geometry pull-coord1-groups pull-coord1-init pull-coord1-k pull-coord1-kB pull-coord1-origin pull-coord1-potential-provider pull-coord1-rate pull-coord1-start pull-coord1-type pull-coord1-vec pull-cylinder-r pull-fout-average pull-group1-name pull-group1-pbcatom pull-group1-weights pull-ncoords pull-ngroups pull-nstfout pull-nstxout pull-pbc-ref-prev-step-com pull-print-com pull-print-components pull-print-ref-value pull-xout-average QMMM qmmm-cp2k-active qmmm-cp2k-qmcharge qmmm-cp2k-qmfilenames qmmm-cp2k-qmgroup qmmm-cp2k-qmmethod qmmm-cp2k-qmmultiplicity QMMM-grps rcoulomb rcoulomb-switch ref-p ref-t refcoord-scaling restraint-lambdas rlist rot-eps0 rot-fit-method0 rot-group0 rot-k0 rot-massw0 rot-min-gauss0 rot-ngroups rot-nstrout rot-nstsout rot-pivot0 rot-potfit-nsteps0 rot-potfit-step0 rot-rate0 rot-slab-dist0 rot-type0 rot-vec0 rotation rtpi rvdw rvdw-switch sc-alpha sc-coul sc-function sc-gapsys-scale-linpoint-lj sc-gapsys-scale-linpoint-q sc-gapsys-sigma-lj sc-power sc-r-power sc-sigma separate-dhdl-file shake-tol sim-temp-high sim-temp-low simulated-tempering simulated-tempering-scaling simulation-part solvent-group split-group0 split-group1 swap-frequency swapcoords symmetrized-transition-matrix table table-extension tau-p tau-t tc-grps tcoupl temperature-lambdas threshold 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

mdrun() (in module gmxapi) MDSession (class in gmxapi._gmxapi) MDSystem (class in gmxapi._gmxapi) mininum-var-min mdp option MissingImplementationError, [1] modify_input() (in module gmxapi) module gmxapi gmxapi._gmxapi gmxapi._logging gmxapi.exceptions gmxapi.simulation gmxapi.utility gmxapi.version scripted_gmx_docker_builds utility morse mdp option MPI (Message Passing Interface) mts mdp option mts-level2-factor mdp option mts-level2-forces mdp option mts-levels mdp option

N

nbfgscorr mdp option nh-chain-length mdp option niter mdp option node nst-transition-matrix mdp option nstcalcenergy 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 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

only OpenCL OpenMP OperationReference (class in gmxapi.abc) orire mdp option orire-fc mdp option

orire-fitgrp mdp option orire-tau mdp option output (gmxapi.abc.OperationReference property) OutputDataProxy (class in gmxapi.simulation.mdrun) (class in gmxapi.simulation.modify_input) (class in gmxapi.simulation.read_tpr)

P

parameters (gmxapi.simulation.mdrun.OutputDataProxy attribute) (gmxapi.simulation.modify_input.OutputDataProxy attribute) (gmxapi.simulation.read_tpr.OutputDataProxy attribute) params() (gmxapi._gmxapi.TprFile method) parser (in module utility) Particle-mesh Ewald path (gmxapi.utility.output attribute) pbc mdp option pcoupl mdp option pcoupltype mdp option periodic-molecules mdp option pme-order mdp option POST_MERGE_ACCEPTANCE prepare_venv() (in module scripted_gmx_docker_builds) print-nose-hoover-chain-variables mdp option ProtocolError, [1] pull mdp option pull-constr-tol mdp option pull-coord1-dim mdp option pull-coord1-dx mdp option pull-coord1-expression 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-potential-provider 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-fout-average 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-pbc-ref-prev-step-com mdp option pull-print-com mdp option pull-print-components mdp option pull-print-ref-value mdp option pull-xout-average mdp option Python Enhancement Proposals PEP 3107 PEP 440

Q

QMMM mdp option qmmm-cp2k-active mdp option qmmm-cp2k-qmcharge mdp option qmmm-cp2k-qmfilenames mdp option

qmmm-cp2k-qmgroup mdp option qmmm-cp2k-qmmethod mdp option qmmm-cp2k-qmmultiplicity mdp option QMMM-grps mdp option

R

rank rcoulomb mdp option rcoulomb-switch mdp option read_tpr() (in module gmxapi) read_tprfile() (in module gmxapi._gmxapi) ref-p mdp option ref-t mdp option refcoord-scaling mdp option REGRESSIONTEST_DOWNLOAD cmake option REGRESSIONTEST_PATH cmake option REGRESSIONTESTBRANCH REGRESSIONTESTCOMMIT restraint-lambdas mdp option result() (gmxapi.abc.Future method) rewrite_tprfile() (in module gmxapi._gmxapi) rlist mdp option rot-eps0 mdp option rot-fit-method0 mdp option rot-group0 mdp option rot-k0 mdp option rot-massw0 mdp option

rot-min-gauss0 mdp option rot-ngroups mdp option rot-nstrout mdp option rot-nstsout mdp option rot-pivot0 mdp option rot-potfit-nsteps0 mdp option rot-potfit-step0 mdp option rot-rate0 mdp option rot-slab-dist0 mdp option rot-type0 mdp option rot-vec0 mdp option rotation mdp option rtpi mdp option rules run() (gmxapi._gmxapi.MDSession method) (gmxapi.abc.OperationReference method) rvdw mdp option rvdw-switch mdp option

S

sc-alpha mdp option sc-coul mdp option sc-function mdp option sc-gapsys-scale-linpoint-lj mdp option sc-gapsys-scale-linpoint-q mdp option sc-gapsys-sigma-lj mdp option sc-power mdp option sc-r-power mdp option sc-sigma mdp option scripted_gmx_docker_builds module separate-dhdl-file mdp option set() (gmxapi._gmxapi.MDArgs method) (gmxapi._gmxapi.SimulationParameters method) setMDArgs() (gmxapi._gmxapi.Context method) shake-tol mdp option shlex_join() (in module scripted_gmx_docker_builds) sim-temp-high mdp option

sim-temp-low mdp option SIMD simulated-tempering mdp option simulated-tempering-scaling mdp option simulation-part mdp option SimulationParameters (class in gmxapi._gmxapi) socket solvent-group mdp option SOURCE_MD5SUM cmake option split-group0 mdp option split-group1 mdp option stderr (gmxapi.simulation.mdrun.OutputDataProxy attribute) stdout (gmxapi.simulation.mdrun.OutputDataProxy attribute) subgraph() (in module gmxapi) swap-frequency mdp option swapcoords mdp option SYCL symmetrized-transition-matrix mdp option

T

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

thread affinity (pinning) threshold mdp option tinit mdp option TprFile (class in gmxapi._gmxapi) trajectory (gmxapi.simulation.mdrun.OutputDataProxy attribute) trigger-post-merge.py command line option --branch --help --regtest-branch --regtest-commit --token --type -h TypeError

U

UnknownException UsageError, [1] 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 utility module

V

ValueError variables 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

Warning when while_loop() (in module gmxapi) wl-oneovert mdp option wl-ratio mdp option wl-scale mdp option write_tprfile() (in module gmxapi._gmxapi)