+++ /dev/null
-; VARIOUS PREPROCESSING OPTIONS
-; Preprocessor information: use cpp syntax.
-; e.g.: -I/home/joe/doe -I/home/mary/roe
-include =
-; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
-define =
-
-; RUN CONTROL PARAMETERS
-integrator = md
-; Start time and timestep in ps
-tinit = 0
-dt = 0.005
-nsteps = 20
-; For exact run continuation or redoing part of a run
-init-step = 0
-; Part index is updated automatically on checkpointing (keeps files separate)
-simulation-part = 1
-; mode for center of mass motion removal
-comm-mode = Linear
-; number of steps for center of mass motion removal
-nstcomm = 100
-; group(s) for center of mass motion removal
-comm-grps =
-
-; LANGEVIN DYNAMICS OPTIONS
-; Friction coefficient (amu/ps) and random seed
-bd-fric = 0
-ld-seed = 1993
-
-; ENERGY MINIMIZATION OPTIONS
-; Force tolerance and initial step-size
-emtol = 10
-emstep = 0.01
-; Max number of iterations in relax-shells
-niter = 20
-; Step size (ps^2) for minimization of flexible constraints
-fcstep = 0
-; Frequency of steepest descents steps when doing CG
-nstcgsteep = 1000
-nbfgscorr = 10
-
-; TEST PARTICLE INSERTION OPTIONS
-rtpi = 0.05
-
-; OUTPUT CONTROL OPTIONS
-; Output frequency for coords (x), velocities (v) and forces (f)
-nstxout = 20
-nstvout = 20
-nstfout = 20
-; Output frequency for energies to log file and energy file
-nstlog = 0
-nstcalcenergy = 100
-nstenergy = 100
-; Output frequency and precision for .xtc file
-nstxtcout = 0
-xtc-precision = 1000
-; This selects the subset of atoms for the .xtc file. You can
-; select multiple groups. By default all atoms will be written.
-xtc-grps =
-; Selection of energy groups
-energygrps =
-
-; NEIGHBORSEARCHING PARAMETERS
-; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs)
-cutoff-scheme = verlet
-; nblist update frequency
-nstlist = 10
-; ns algorithm (simple or grid)
-ns-type = Grid
-; Periodic boundary conditions: xyz, no, xy
-pbc = xyz
-periodic-molecules = no
-; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom,
-; a value of -1 means: use rlist
-verlet-buffer-drift = -1
-; nblist cut-off
-rlist = 0.9
-; long-range cut-off for switched potentials
-rlistlong = -1
-nstcalclr = -1
-
-; OPTIONS FOR ELECTROSTATICS AND VDW
-; Method for doing electrostatics
-coulombtype = PME
-coulomb-modifier = Potential-shift-Verlet
-rcoulomb-switch = 0
-rcoulomb = 0.85
-; Relative dielectric constant for the medium and the reaction field
-epsilon-r = 1
-epsilon-rf = 0
-; Method for doing Van der Waals
-vdw-type = Cut-off
-vdw-modifier = Potential-shift-Verlet
-; cut-off lengths
-rvdw-switch = 0
-rvdw = 0.85
-; Apply long range dispersion corrections for Energy and Pressure
-DispCorr = No
-; Extension of the potential lookup tables beyond the cut-off
-table-extension = 1
-; Seperate tables between energy group pairs
-energygrp-table =
-; Spacing for the PME/PPPM FFT grid
-fourierspacing = 0.12
-; FFT grid size, when a value is 0 fourierspacing will be used
-fourier_nx = 24
-fourier_ny = 24
-fourier_nz = 24
-; EWALD/PME/PPPM parameters
-pme-order = 4
-ewald-rtol = 1e-05
-ewald-geometry = 3d
-epsilon-surface = 0
-optimize-fft = no
-
-; IMPLICIT SOLVENT ALGORITHM
-implicit-solvent = No
-
-; GENERALIZED BORN ELECTROSTATICS
-; Algorithm for calculating Born radii
-gb-algorithm = Still
-; Frequency of calculating the Born radii inside rlist
-nstgbradii = 1
-; Cutoff for Born radii calculation; the contribution from atoms
-; between rlist and rgbradii is updated every nstlist steps
-rgbradii = 1
-; Dielectric coefficient of the implicit solvent
-gb-epsilon-solvent = 80
-; Salt concentration in M for Generalized Born models
-gb-saltconc = 0
-; Scaling factors used in the OBC GB model. Default values are OBC(II)
-gb-obc-alpha = 1
-gb-obc-beta = 0.8
-gb-obc-gamma = 4.85
-gb-dielectric-offset = 0.009
-sa-algorithm = Ace-approximation
-; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
-; The value -1 will set default value for Still/HCT/OBC GB-models.
-sa-surface-tension = -1
-
-; OPTIONS FOR WEAK COUPLING ALGORITHMS
-; Temperature coupling
-tcoupl = v-rescale
-nsttcouple = -1
-nh-chain-length = 10
-print-nose-hoover-chain-variables = no
-; Groups to couple separately
-tc_grps = system
-; Time constant (ps) and reference temperature (K)
-tau_t = 0.1
-ref_t = 300
-; pressure coupling
-Pcoupl = Berendsen
-pcoupltype = Isotropic
-nstpcouple = -1
-; Time constant (ps), compressibility (1/bar) and reference P (bar)
-tau_p = 1
-compressibility = 4.5e-5
-ref_p = 1
-; Scaling of reference coordinates, No, All or COM
-refcoord-scaling = No
-
-; OPTIONS FOR QMMM calculations
-QMMM = no
-; Groups treated Quantum Mechanically
-QMMM-grps =
-; QM method
-QMmethod =
-; QMMM scheme
-QMMMscheme = normal
-; QM basisset
-QMbasis =
-; QM charge
-QMcharge =
-; QM multiplicity
-QMmult =
-; Surface Hopping
-SH =
-; CAS space options
-CASorbitals =
-CASelectrons =
-SAon =
-SAoff =
-SAsteps =
-; Scale factor for MM charges
-MMChargeScaleFactor = 1
-
-; SIMULATED ANNEALING
-; Type of annealing for each temperature group (no/single/periodic)
-annealing =
-; Number of time points to use for specifying annealing in each group
-annealing-npoints =
-; List of times at the annealing points for each group
-annealing-time =
-; Temp. at each annealing point, for each group.
-annealing-temp =
-
-; GENERATE VELOCITIES FOR STARTUP RUN
-gen-vel = no
-gen-temp = 300
-gen-seed = 173529
-
-; OPTIONS FOR BONDS
-constraints = all-bonds
-; Type of constraint algorithm
-constraint-algorithm = Lincs
-; Do not constrain the start configuration
-continuation = no
-; Use successive overrelaxation to reduce the number of shake iterations
-Shake-SOR = no
-; Relative tolerance of shake
-shake-tol = 0.0001
-; Highest order in the expansion of the constraint coupling matrix
-lincs_order = 2
-; Number of iterations in the final step of LINCS. 1 is fine for
-; normal simulations, but use 2 to conserve energy in NVE runs.
-; For energy minimization with constraints it should be 4 to 8.
-lincs_iter = 5
-; Lincs will write a warning to the stderr if in one step a bond
-; rotates over more degrees than
-lincs-warnangle = 30
-; Convert harmonic bonds to morse potentials
-morse = no
-
-; ENERGY GROUP EXCLUSIONS
-; Pairs of energy groups for which all non-bonded interactions are excluded
-energygrp-excl =
-
-; WALLS
-; Number of walls, type, atom types, densities and box-z scale factor for Ewald
-nwall = 0
-wall-type = 9-3
-wall-r-linpot = -1
-wall-atomtype =
-wall-density =
-wall-ewald-zfac = 3
-
-; COM PULLING
-; Pull type: no, umbrella, constraint or constant-force
-pull = no
-
-; ENFORCED ROTATION
-; Enforced rotation: No or Yes
-rotation = no
-
-; NMR refinement stuff
-; Distance restraints type: No, Simple or Ensemble
-disre = No
-; Force weighting of pairs in one distance restraint: Conservative or Equal
-disre-weighting = Conservative
-; Use sqrt of the time averaged times the instantaneous violation
-disre-mixed = no
-disre-fc = 1000
-disre-tau = 0
-; Output frequency for pair distances to energy file
-nstdisreout = 100
-; Orientation restraints: No or Yes
-orire = no
-; Orientation restraints force constant and tau for time averaging
-orire-fc = 0
-orire-tau = 0
-orire-fitgrp =
-; Output frequency for trace(SD) and S to energy file
-nstorireout = 100
-
-; Free energy variables
-free-energy = no
-couple-moltype =
-couple-lambda0 = vdw-q
-couple-lambda1 = vdw-q
-couple-intramol = no
-init-lambda = -1
-init-lambda-state = 0
-delta-lambda = 0
-nstdhdl = 100
-fep-lambdas =
-mass-lambdas =
-coul-lambdas =
-vdw-lambdas =
-bonded-lambdas =
-restraint-lambdas =
-temperature-lambdas =
-init-lambda-weights =
-dhdl-print-energy = no
-sc-alpha = 0
-sc-power = 1
-sc-r-power = 6
-sc-sigma = 0.3
-sc-coul = no
-separate-dhdl-file = yes
-dhdl-derivatives = yes
-dh_hist_size = 0
-dh_hist_spacing = 0.1
-
-; Non-equilibrium MD stuff
-acc-grps =
-accelerate =
-freezegrps =
-freezedim =
-cos-acceleration = 0
-deform =
-
-; simulated tempering variables
-simulated-tempering = no
-simulated-tempering-scaling = geometric
-sim-temp-low = 300
-sim-temp-high = 300
-
-; Electric fields
-; Format is number of terms (int) and for all terms an amplitude (real)
-; and a phase angle (real)
-E-x =
-E-xt =
-E-y =
-E-yt =
-E-z =
-E-zt =
-
-; AdResS parameters
-adress = no
-
-; User defined thingies
-user1-grps =
-user2-grps =
-userint1 = 0
-userint2 = 0
-userint3 = 0
-userint4 = 0
-userreal1 = 0
-userreal2 = 0
-userreal3 = 0
-userreal4 = 0
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
std::string reducedPrecisionTrajectoryFileName_;
std::string groOutputFileName_;
std::string ndxFileName_;
- std::string mdpInputFileName_;
+ std::string mdpInputFileName_; /**< This file is temporary and will be overwritten with mdpInputContents_ when calling grompp.
+ * TODO: remove this when the multisim tests use -multidir.
+ */
std::string mdpOutputFileName_;
std::string tprFileName_;
std::string logFileName_;
std::string swapFileName_;
int nsteps_;
//@}
+ //! What will be written into mdpInputFileName_ before the grompp call
+ std::string mdpInputContents_;
private:
TestFileManager &fileManager_;
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff