;
; File 'mdout.mdp' was generated
-; By user: spoel (291)
-; On host: chagall
-; At date: Mon Dec 15 13:13:06 2003
+; By user: alexxy (1000)
+; On host: x201
+; At date: Wed Oct 12 02:06:35 2011
;
; VARIOUS PREPROCESSING OPTIONS
-title = Yo
-cpp = /usr/bin/cpp
+; 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
nsteps = 10000
; 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 = 1
+nstcomm = 10
; group(s) for center of mass motion removal
comm-grps =
; LANGEVIN DYNAMICS OPTIONS
-; Temperature, friction coefficient (amu/ps) and random seed
-bd-temp = 300
+; Friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = 1993
emstep = 0.01
; Max number of iterations in relax_shells
niter = 20
-; Step size (1/ps^2) for minimization of flexible constraints
+; 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
-; Checkpointing helps you continue after crashes
-nstcheckpoint = 1000
; Output frequency for energies to log file and energy file
nstlog = 50
+nstcalcenergy = -1
nstenergy = 50
-; Output frequency and precision for xtc file
+; Output frequency and precision for .xtc file
nstxtcout = 50
xtc-precision = 1000
-; This selects the subset of atoms for the xtc file. You can
+; 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
nstlist = 5
; ns algorithm (simple or grid)
ns_type = grid
-; Periodic boundary conditions: xyz (default), no (vacuum)
-; or full (infinite systems only)
+; Periodic boundary conditions: xyz, no, xy
pbc = xyz
+periodic_molecules = no
; nblist cut-off
rlist = 0.9
-domain-decomposition = no
+; long-range cut-off for switched potentials
+rlistlong = -1
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Cut-off
rcoulomb-switch = 0
rcoulomb = 0.9
-; Dielectric constant (DC) for cut-off or DC of reaction field
+; Relative dielectric constant for the medium and the reaction field
epsilon-r = 1
+epsilon_rf = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
DispCorr = EnerPres
; 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
epsilon_surface = 0
optimize_fft = no
+; IMPLICIT SOLVENT ALGORITHM
+implicit_solvent = No
+
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
+; Dielectric coefficient of the implicit solvent
+gb_epsilon_solvent = 80
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
-
-; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
-implicit_solvent = No
+; 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 = berendsen
+nsttcouple = -1
+nh-chain-length = 10
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = isotropic
+nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
+; Scaling of reference coordinates, No, All or COM
+refcoord_scaling = No
; Random seed for Andersen thermostat
andersen_seed = 815131
+; 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
+; Optimization of QM subsystem
+bOPT =
+bTS =
+
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing = no
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
-unconstrained-start = no
+continuation = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
; 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
+
; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre = No
orire-fc = 0
orire-tau = 0
orire-fitgrp =
-; Output frequency for trace(SD) to energy file
+; Output frequency for trace(SD) and S to energy file
nstorireout = 100
-; Dihedral angle restraints: No, Simple or Ensemble
+; Dihedral angle restraints: No or Yes
dihre = No
dihre-fc = 1000
-dihre-tau = 0
-; Output frequency for dihedral values to energy file
-nstdihreout = 100
; Free energy control stuff
free-energy = no
init-lambda = 0
delta-lambda = 0
+foreign_lambda =
sc-alpha = 0
+sc-power = 0
sc-sigma = 0.3
+nstdhdl = 10
+separate-dhdl-file = yes
+dhdl-derivatives = yes
+dh_hist_size = 0
+dh_hist_spacing = 0.1
+couple-moltype =
+couple-lambda0 = vdw-q
+couple-lambda1 = vdw-q
+couple-intramol = no
; Non-equilibrium MD stuff
acc-grps =
freezegrps =
freezedim =
cos-acceleration = 0
+deform =
; Electric fields
; Format is number of terms (int) and for all terms an amplitude (real)
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff