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330 lines
11 KiB
330 lines
11 KiB
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; File 'mdout.mdp' was generated |
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; By user: unknown (1104) |
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; On host: cmmd |
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; At date: Tue Jun 7 16:54:19 2022 |
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; |
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; Created by: |
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; :-) GROMACS - gmx grompp, 2020.6-Debian-2020.6-2 (-: |
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; |
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; Executable: /usr/bin/gmx |
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; Data prefix: /usr |
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; Working dir: /home/student/adit/CMMDE_launching/larutan/SistemLarutan |
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; Command line: |
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; gmx -quiet grompp -c npt.gro -f nvep.mdp -maxwarn 2 -o nvep.tpr -p system_GMX.top |
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; VARIOUS PREPROCESSING OPTIONS |
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; Preprocessor information: use cpp syntax. |
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; e.g.: -I/home/joe/doe -I/home/mary/roe |
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include = |
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; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive) |
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define = |
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; RUN CONTROL PARAMETERS |
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integrator = md |
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; Start time and timestep in ps |
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tinit = 0 |
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dt = 0.0005 |
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nsteps = 10000 |
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; For exact run continuation or redoing part of a run |
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init-step = 0 |
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; Part index is updated automatically on checkpointing (keeps files separate) |
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simulation-part = 1 |
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; mode for center of mass motion removal |
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comm-mode = Linear |
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; number of steps for center of mass motion removal |
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nstcomm = 100 |
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; group(s) for center of mass motion removal |
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comm-grps = |
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; LANGEVIN DYNAMICS OPTIONS |
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; Friction coefficient (amu/ps) and random seed |
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bd-fric = 0 |
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ld-seed = -1 |
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; ENERGY MINIMIZATION OPTIONS |
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; Force tolerance and initial step-size |
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emtol = 10 |
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emstep = 0.01 |
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; Max number of iterations in relax-shells |
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niter = 20 |
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; Step size (ps^2) for minimization of flexible constraints |
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fcstep = 0 |
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; Frequency of steepest descents steps when doing CG |
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nstcgsteep = 1000 |
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nbfgscorr = 10 |
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; TEST PARTICLE INSERTION OPTIONS |
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rtpi = 0.05 |
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; OUTPUT CONTROL OPTIONS |
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; Output frequency for coords (x), velocities (v) and forces (f) |
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nstxout = 500 |
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nstvout = 500 |
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nstfout = 0 |
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; Output frequency for energies to log file and energy file |
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nstlog = 500 |
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nstcalcenergy = 100 |
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nstenergy = 500 |
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; Output frequency and precision for .xtc file |
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nstxout-compressed = 0 |
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compressed-x-precision = 1000 |
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; This selects the subset of atoms for the compressed |
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; trajectory file. You can select multiple groups. By |
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; default, all atoms will be written. |
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compressed-x-grps = |
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; Selection of energy groups |
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energygrps = |
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; NEIGHBORSEARCHING PARAMETERS |
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; cut-off scheme (Verlet: particle based cut-offs) |
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cutoff-scheme = Verlet |
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; nblist update frequency |
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nstlist = 10 |
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; Periodic boundary conditions: xyz, no, xy |
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pbc = xyz |
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periodic-molecules = no |
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; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom, |
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; a value of -1 means: use rlist |
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verlet-buffer-tolerance = 0.005 |
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; nblist cut-off |
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rlist = 1 |
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; long-range cut-off for switched potentials |
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; OPTIONS FOR ELECTROSTATICS AND VDW |
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; Method for doing electrostatics |
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coulombtype = PME |
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coulomb-modifier = Potential-shift-Verlet |
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rcoulomb-switch = 0 |
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rcoulomb = 0.9613990804113833 |
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; Relative dielectric constant for the medium and the reaction field |
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epsilon-r = 1 |
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epsilon-rf = 0 |
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; Method for doing Van der Waals |
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vdw-type = Cut-off |
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vdw-modifier = Potential-shift-Verlet |
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; cut-off lengths |
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rvdw-switch = 0 |
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rvdw = 0.9613990804113833 |
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; Apply long range dispersion corrections for Energy and Pressure |
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DispCorr = EnerPres |
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; Extension of the potential lookup tables beyond the cut-off |
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table-extension = 1 |
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; Separate tables between energy group pairs |
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energygrp-table = |
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; Spacing for the PME/PPPM FFT grid |
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fourierspacing = 0.16 |
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; FFT grid size, when a value is 0 fourierspacing will be used |
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fourier-nx = 0 |
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fourier-ny = 0 |
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fourier-nz = 0 |
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; EWALD/PME/PPPM parameters |
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pme_order = 4 |
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ewald-rtol = 1e-05 |
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ewald-rtol-lj = 0.001 |
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lj-pme-comb-rule = Geometric |
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ewald-geometry = 3d |
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epsilon-surface = 0 |
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implicit-solvent = no |
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; OPTIONS FOR WEAK COUPLING ALGORITHMS |
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; Temperature coupling |
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tcoupl = no |
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nsttcouple = -1 |
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nh-chain-length = 10 |
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print-nose-hoover-chain-variables = no |
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; Groups to couple separately |
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tc-grps = |
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; Time constant (ps) and reference temperature (K) |
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tau-t = |
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ref-t = |
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; pressure coupling |
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pcoupl = no |
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pcoupltype = Isotropic |
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nstpcouple = -1 |
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; Time constant (ps), compressibility (1/bar) and reference P (bar) |
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tau-p = 1 |
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compressibility = |
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ref-p = |
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; Scaling of reference coordinates, No, All or COM |
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refcoord-scaling = No |
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; OPTIONS FOR QMMM calculations |
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QMMM = no |
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; Groups treated Quantum Mechanically |
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QMMM-grps = |
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; QM method |
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QMmethod = |
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; QMMM scheme |
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QMMMscheme = normal |
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; QM basisset |
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QMbasis = |
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; QM charge |
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QMcharge = |
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; QM multiplicity |
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QMmult = |
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; Surface Hopping |
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SH = |
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; CAS space options |
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CASorbitals = |
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CASelectrons = |
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SAon = |
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SAoff = |
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SAsteps = |
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; Scale factor for MM charges |
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MMChargeScaleFactor = 1 |
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; SIMULATED ANNEALING |
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; Type of annealing for each temperature group (no/single/periodic) |
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annealing = |
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; Number of time points to use for specifying annealing in each group |
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annealing-npoints = |
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; List of times at the annealing points for each group |
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annealing-time = |
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; Temp. at each annealing point, for each group. |
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annealing-temp = |
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; GENERATE VELOCITIES FOR STARTUP RUN |
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gen_vel = no |
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gen-temp = 300 |
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gen-seed = -1 |
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; OPTIONS FOR BONDS |
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constraints = none |
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; Type of constraint algorithm |
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constraint-algorithm = Lincs |
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; Do not constrain the start configuration |
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continuation = yes |
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; Use successive overrelaxation to reduce the number of shake iterations |
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Shake-SOR = no |
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; Relative tolerance of shake |
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shake-tol = 0.0001 |
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; Highest order in the expansion of the constraint coupling matrix |
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lincs-order = 4 |
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; Number of iterations in the final step of LINCS. 1 is fine for |
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; normal simulations, but use 2 to conserve energy in NVE runs. |
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; For energy minimization with constraints it should be 4 to 8. |
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lincs-iter = 1 |
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; Lincs will write a warning to the stderr if in one step a bond |
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; rotates over more degrees than |
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lincs-warnangle = 30 |
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; Convert harmonic bonds to morse potentials |
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morse = no |
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; ENERGY GROUP EXCLUSIONS |
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; Pairs of energy groups for which all non-bonded interactions are excluded |
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energygrp-excl = |
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; WALLS |
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; Number of walls, type, atom types, densities and box-z scale factor for Ewald |
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nwall = 0 |
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wall-type = 9-3 |
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wall-r-linpot = -1 |
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wall-atomtype = |
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wall-density = |
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wall-ewald-zfac = 3 |
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; COM PULLING |
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pull = no |
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; AWH biasing |
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awh = no |
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; ENFORCED ROTATION |
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; Enforced rotation: No or Yes |
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rotation = no |
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; Group to display and/or manipulate in interactive MD session |
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IMD-group = |
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; NMR refinement stuff |
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; Distance restraints type: No, Simple or Ensemble |
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disre = No |
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; Force weighting of pairs in one distance restraint: Conservative or Equal |
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disre-weighting = Conservative |
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; Use sqrt of the time averaged times the instantaneous violation |
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disre-mixed = no |
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disre-fc = 1000 |
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disre-tau = 0 |
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; Output frequency for pair distances to energy file |
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nstdisreout = 100 |
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; Orientation restraints: No or Yes |
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orire = no |
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; Orientation restraints force constant and tau for time averaging |
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orire-fc = 0 |
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orire-tau = 0 |
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orire-fitgrp = |
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; Output frequency for trace(SD) and S to energy file |
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nstorireout = 100 |
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; Free energy variables |
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free-energy = no |
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couple-moltype = |
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couple-lambda0 = vdw-q |
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couple-lambda1 = vdw-q |
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couple-intramol = no |
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init-lambda = -1 |
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init-lambda-state = -1 |
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delta-lambda = 0 |
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nstdhdl = 50 |
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fep-lambdas = |
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mass-lambdas = |
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coul-lambdas = |
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vdw-lambdas = |
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bonded-lambdas = |
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restraint-lambdas = |
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temperature-lambdas = |
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calc-lambda-neighbors = 1 |
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init-lambda-weights = |
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dhdl-print-energy = no |
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sc-alpha = 0 |
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sc-power = 1 |
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sc-r-power = 6 |
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sc-sigma = 0.3 |
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sc-coul = no |
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separate-dhdl-file = yes |
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dhdl-derivatives = yes |
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dh_hist_size = 0 |
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dh_hist_spacing = 0.1 |
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; Non-equilibrium MD stuff |
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acc-grps = |
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accelerate = |
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freezegrps = |
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freezedim = |
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cos-acceleration = 0 |
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deform = |
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; simulated tempering variables |
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simulated-tempering = no |
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simulated-tempering-scaling = geometric |
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sim-temp-low = 300 |
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sim-temp-high = 300 |
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; Ion/water position swapping for computational electrophysiology setups |
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; Swap positions along direction: no, X, Y, Z |
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swapcoords = no |
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adress = no |
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; User defined thingies |
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user1-grps = |
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user2-grps = |
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userint1 = 0 |
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userint2 = 0 |
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userint3 = 0 |
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userint4 = 0 |
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userreal1 = 0 |
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userreal2 = 0 |
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userreal3 = 0 |
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userreal4 = 0 |
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; Electric fields |
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; Format for electric-field-x, etc. is: four real variables: |
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; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps), |
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; and sigma (ps) width of the pulse. Omega = 0 means static field, |
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; sigma = 0 means no pulse, leaving the field to be a cosine function. |
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electric-field-x = 0 0 0 0 |
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electric-field-y = 0 0 0 0 |
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electric-field-z = 0 0 0 0 |
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; Density guided simulation |
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density-guided-simulation-active = false
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