Index

A

acc-grps mdp option accelerate mdp option adress mdp option annealing mdp option annealing-npoints mdp option annealing-temp mdp option annealing-time mdp option 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-period 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

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

bulk-offsetA mdp option bulk-offsetB mdp option

C

cache calc-lambda-neighbors mdp option CASelectrons mdp option CASorbitals mdp option cmake option BUILD_TESTING CMAKE_INSTALL_LIBDIR 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_CLANG_CUDA GMX_COMPACT_DOXYGEN GMX_COMPILER_WARNINGS GMX_CUDA_CLANG_FLAGS GMX_CYCLE_SUBCOUNTERS GMX_DEVELOPER_BUILD GMX_DOUBLE GMX_EXTERNAL_BLAS GMX_EXTERNAL_LAPACK GMX_EXTERNAL_TNG GMX_EXTRAE GMX_FFT_LIBRARY GMX_GIT_VERSION_INFO GMX_GPU GMX_INSTALL_DATASUBDIR GMX_LOAD_PLUGINS GMX_MPI GMX_OPENMP GMX_PREFER_STATIC_LIBS GMX_RELAXED_DOUBLE_PRECISION 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 CMAKE_INSTALL_LIBDIR cmake option

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 coupl-steps 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 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

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 dt mdp option

E

electric-field-x electric-field-y ; electric-field-z; mdp option electric-field-y ; electric-field-z; mdp option electric-field-x 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_CLANG_CUDA 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_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_LOAD_PLUGINS cmake option GMX_MPI cmake option GMX_OPENMP cmake option GMX_PREFER_STATIC_LIBS cmake option GMX_RELAXED_DOUBLE_PRECISION 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 iontype0-in-A mdp option iontype0-in-B mdp option iontype0-name mdp option iontypes 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 massw-split0 mdp option massw-split1 mdp option mc-temperature mdp option mdp option CASelectrons CASorbitals DispCorr QMMM QMMM-grps QMMMscheme QMbasis QMcharge QMmethod QMmult SH 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-period 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 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 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 nbfgscorr nh-chain-length niter ns-type nst-transition-matrix nstcalcenergy 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 print-nose-hoover-chain-variables 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-potential-provider pull-coord1-rate pull-coord1-start pull-coord1-type pull-coord1-vec pull-cylinder-r pull-group1-name pull-group1-pbcatom pull-group1-slice-smooth pull-group1-slice-x-max pull-group1-slice-x-min pull-group1-sliced pull-group1-weights pull-ncoords pull-ngroups pull-nstfout pull-nstxout pull-print-com pull-print-components pull-print-ref-value rcoulomb rcoulomb-switch ref-p ref-t refcoord-scaling restraint-lambdas rgbradii 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 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 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

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 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

OpenCL OpenMP orire mdp option orire-fc mdp option

orire-fitgrp mdp option orire-tau mdp option

P

pbc mdp option pcoupl mdp option pcoupltype mdp option periodic-molecules mdp option pme-order mdp option print-nose-hoover-chain-variables 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-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-group1-name mdp option pull-group1-pbcatom mdp option pull-group1-slice-smooth mdp option pull-group1-slice-x-max mdp option pull-group1-slice-x-min mdp option pull-group1-sliced 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-com 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 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 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 simulation-part mdp option socket solvent-group mdp option SOURCE_MD5SUM cmake option split-group0 mdp option split-group1 mdp option swap-frequency mdp option swapcoords mdp 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 thread affinity (pinning) threshold mdp option 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