Index

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