--- /dev/null
-
-; 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
+ <?xml version="1.0"?>
+ <?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+ <ReferenceData>
+ <Bool Name="Error parsing mdp file">false</Bool>
+ <String Name="OutputMdpFile">
+ ; 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 = -DBOOL -DVAR=VALUE
+
+ ; RUN CONTROL PARAMETERS
+ integrator = md
+ ; Start time and timestep in ps
+ tinit = 0
+ dt = 0.001
+ nsteps = 0
+ ; 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 = -1
+
+ ; 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 = 0
+ nstvout = 0
+ nstfout = 0
+ ; Output frequency for energies to log file and energy file
+ nstlog = 1000
+ nstcalcenergy = 100
+ nstenergy = 1000
+ ; Output frequency and precision for .xtc file
+ nstxout-compressed = 0
+ compressed-x-precision = 1000
+ ; This selects the subset of atoms for the compressed
+ ; trajectory file. You can select multiple groups. By
+ ; default, all atoms will be written.
+ compressed-x-grps =
+ ; Selection of energy groups
+ energygrps =
+
+ ; NEIGHBORSEARCHING PARAMETERS
+ ; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
+ 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 error due to the Verlet buffer in kJ/mol/ps per atom,
+ ; a value of -1 means: use rlist
+ verlet-buffer-tolerance = 0.005
+ ; nblist cut-off
+ rlist = 1
+ ; long-range cut-off for switched potentials
+
+ ; OPTIONS FOR ELECTROSTATICS AND VDW
+ ; Method for doing electrostatics
+ coulombtype = Cut-off
+ coulomb-modifier = Potential-shift-Verlet
+ rcoulomb-switch = 0
+ rcoulomb = 1
+ ; 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 = 1
+ ; Apply long range dispersion corrections for Energy and Pressure
+ DispCorr = No
+ ; Extension of the potential lookup tables beyond the cut-off
+ table-extension = 1
+ ; Separate 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 = 0
+ fourier-ny = 0
+ fourier-nz = 0
+ ; EWALD/PME/PPPM parameters
+ pme-order = 4
+ ewald-rtol = 1e-05
+ ewald-rtol-lj = 0.001
+ lj-pme-comb-rule = Geometric
+ ewald-geometry = 3d
+ epsilon-surface = 0
++implicit-solvent = no
+
+ ; OPTIONS FOR WEAK COUPLING ALGORITHMS
+ ; Temperature coupling
+ tcoupl = No
+ nsttcouple = -1
+ nh-chain-length = 10
+ print-nose-hoover-chain-variables = no
+ ; Groups to couple separately
+ tc-grps =
+ ; Time constant (ps) and reference temperature (K)
+ tau-t =
+ ref-t =
+ ; pressure coupling
+ pcoupl = No
+ pcoupltype = Isotropic
+ nstpcouple = -1
+ ; Time constant (ps), compressibility (1/bar) and reference P (bar)
+ tau-p = 1
+ compressibility =
+ ref-p =
+ ; 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 = -1
+
+ ; OPTIONS FOR BONDS
+ constraints = none
+ ; 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 = 4
+ ; 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 = 1
+ ; 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 = no
+
+ ; AWH biasing
+ awh = no
+
+ ; ENFORCED ROTATION
+ ; Enforced rotation: No or Yes
+ rotation = no
+
+ ; Group to display and/or manipulate in interactive MD session
+ IMD-group =
+
+ ; 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 = -1
+ delta-lambda = 0
+ nstdhdl = 50
+ fep-lambdas =
+ mass-lambdas =
+ coul-lambdas =
+ vdw-lambdas =
+ bonded-lambdas =
+ restraint-lambdas =
+ temperature-lambdas =
+ calc-lambda-neighbors = 1
+ 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
+
+ ; Ion/water position swapping for computational electrophysiology setups
+ ; Swap positions along direction: no, X, Y, Z
+ swapcoords = no
+ 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
+ ; Electric fields
+ ; Format for electric-field-x, etc. is: four real variables:
+ ; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps),
+ ; and sigma (ps) width of the pulse. Omega = 0 means static field,
+ ; sigma = 0 means no pulse, leaving the field to be a cosine function.
+ electric-field-x = 0 0 0 0
+ electric-field-y = 0 0 0 0
+ electric-field-z = 0 0 0 0
+ </String>
+ </ReferenceData>
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff