Default values are given in parentheses. The first option in the list is always the default option. Units are given in square brackets The difference between a dash and an underscore is ignored. A sample .mdp file is available. This should be appropriate to start a normal simulation. Edit it to suit your specific needs and desires. acc-grps accelerate annealing annealing-npoints annealing-time annealing-temp bd-fric bDispCorr comm-mode comm-grps compressibility constraint-algorithm constraints cos-acceleration coulombtype coulomb-modifier couple-intramol couple-lambda0 couple-lambda1 couple-moltype cutoff-scheme define deform delta-lambda disre disre-weighting disre-mixed disre-fc disre-tau dt emstep emtol energygrp-excl energygrp-table energygrps epsilon-r epsilon-rf ewald-rtol ewald-geometry epsilon-surface E-x E-xt E-y E-yt E-z E-zt fcstep fourier-nx fourier-ny fourier-nz fourierspacing free-energy freezedim freezegrps gen-seed gen-temp gen-vel include init-lambda init-lambda-weights init-step initial-wl-delta integrator ld-seed lincs-iter lincs-order lincs-warnangle lmc-forced-nstart lmc-gibbsdelta lmc-mc-move lmc-seed lmc-stats lmc-weights-equil mc-temperature mininum-var-min morse nbfgscorr niter nh-chain-length nstcgsteep nstcalcenergy nstcomm nstdisreout nstenergy nsteps nstfout nstlist nstlog nstpcouple nsttcouple nstvout nstxout nstxout-compressed nst-transition-matrix ns-type nwall orire orire-fc orire-tau orire-fitgrp nstorireout pbc pcoupl pcoupltype periodic-molecules pme-order pull refcoord-scaling ref-p ref-t rcoulomb-switch rcoulomb rlist rlistlong rtpi rvdw-switch rvdw sc-alpha sc-power sc-sigma shake-tol sim-temp-low sim-temp-high simulated-tempering simulated-tempering-scaling symmetrized-transition-matrix table-extension tau-p tau-t tc-grps tcoupl tinit continuation user1-grps user2-grps userint1 userint2 userint3 userint4 userreal1 userreal2 userreal3 userreal4 vdwtype vdw-modifier verlet-buffer-tolerance compressed-x-grps compressed-x-precision zero-temp-time wall-atomtype wall-density wall-ewald-zfac wall-r-linpot wall-type weight-equil-count-ratio weight-equil-number-all-lambda weight-equil-number-samples weight-equil-number-steps weight-equil-wl-delta wl-ratio wl-scale Source.

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