Allow parameter reading from files and update data
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
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;
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; Generated by:
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; Vitaly V. Chaban
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; School of Chemistry
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; University of Kharkiv
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; Ukraine, Kharkiv-61077, Svoboda sq., 4
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; email: chaban@univer.kharkov.ua, vvchaban@gmail.com
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; skype: vvchaban
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; System: Liquid argon (1000 atoms) at 80 K. Equilibrated for 500ps.
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; VARIOUS PREPROCESSING OPTIONS
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title = Yo
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cpp = /usr/bin/cpp
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include =
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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 = 0.001
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nsteps = 250000
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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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; 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 = 1
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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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; Temperature, friction coefficient (amu/ps) and random seed
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bd-temp = 300
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bd-fric = 0
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ld-seed = 1993
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; ENERGY MINIMIZATION OPTIONS
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; Force tolerance and initial step-size
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emtol = 100
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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 (1/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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; 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 = 5
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nstfout = 0
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; Checkpointing helps you continue after crashes
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nstcheckpoint = 1000
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; Output frequency for energies to log file and energy file
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nstlog = 50
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nstenergy = 50
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; Output frequency and precision for xtc file
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nstxtcout = 5
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xtc-precision = 1000
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; This selects the subset of atoms for the xtc file. You can
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; select multiple groups. By default all atoms will be written.
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xtc-grps =
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; Selection of energy groups
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energygrps =
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; NEIGHBORSEARCHING PARAMETERS
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; nblist update frequency
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nstlist = 5
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; ns algorithm (simple or grid)
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ns_type = grid
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; Periodic boundary conditions: xyz (default), no (vacuum)
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; or full (infinite systems only)
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pbc = xyz
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; nblist cut-off
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rlist = 0.9
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domain-decomposition = no
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; OPTIONS FOR ELECTROSTATICS AND VDW
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; Method for doing electrostatics
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coulombtype = Cut-off
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rcoulomb-switch = 0
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rcoulomb = 0.9
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; Dielectric constant (DC) for cut-off or DC of reaction field
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epsilon-r = 1
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; Method for doing Van der Waals
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vdw-type = Cut-off
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; cut-off lengths
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rvdw-switch = 0
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rvdw = 0.9
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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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; Spacing for the PME/PPPM FFT grid
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fourierspacing = 0.12
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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_geometry = 3d
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epsilon_surface = 0
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optimize_fft = no
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; GENERALIZED BORN ELECTROSTATICS
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; Algorithm for calculating Born radii
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gb_algorithm = Still
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; Frequency of calculating the Born radii inside rlist
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nstgbradii = 1
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; Cutoff for Born radii calculation; the contribution from atoms
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; between rlist and rgbradii is updated every nstlist steps
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rgbradii = 2
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; Salt concentration in M for Generalized Born models
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gb_saltconc = 0
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; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
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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 = berendsen
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; Groups to couple separately
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tc-grps = System
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; Time constant (ps) and reference temperature (K)
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tau_t = 0.1
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ref_t = 80
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; Pressure coupling
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Pcoupl = no
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Pcoupltype = isotropic
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; Time constant (ps), compressibility (1/bar) and reference P (bar)
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tau_p = 1.0
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compressibility = 4.5e-5
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ref_p = 1.0
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; Random seed for Andersen thermostat
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andersen_seed = 815131
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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 = no
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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 = yes
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gen_temp = 80
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gen_seed = 1993
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; OPTIONS FOR BONDS
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constraints = all-bonds
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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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unconstrained-start = no
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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 = 1e-04
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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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; 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) to energy file
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nstorireout = 100
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; Dihedral angle restraints: No, Simple or Ensemble
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dihre = No
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dihre-fc = 1000
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dihre-tau = 0
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; Output frequency for dihedral values to energy file
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nstdihreout = 100
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; Free energy control stuff
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free-energy = no
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init-lambda = 0
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delta-lambda = 0
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sc-alpha = 0
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sc-sigma = 0.3
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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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; Electric fields
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; Format is number of terms (int) and for all terms an amplitude (real)
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; and a phase angle (real)
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E-x =
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E-xt =
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E-y =
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E-yt =
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E-z =
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E-zt =
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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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@@ -0,0 +1,10 @@
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mass 39.94
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sigma 0.0062220
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epsilon 0.0000096960
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ntimes 1000
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dt 0.001
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temp 80
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x_out_freq 500
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v_out_freq 5
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cutforce 9.0
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reneigh_every 5
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