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331 lines
11 KiB
331 lines
11 KiB
2 years ago
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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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