1; RUN CONTROL PARAMETERS
2integrator               = sd
3; Start time and timestep in ps
4tinit                    = 0
5dt                       = 0.004
6nsteps                   = 250000
7; For exact run continuation or redoing part of a run
8init_step                = 0
9; mode for center of mass motion removal
10comm-mode                = Linear
11; number of steps for center of mass motion removal
12nstcomm                  = 1
13; group(s) for center of mass motion removal
14comm-grps                =
15
16; OUTPUT CONTROL OPTIONS
17; Output frequency for coords (x), velocities (v) and fo_ces (f)
18nstxout                  = 0
19nstvout                  = 0
20nstfout                  = 0
21; Output frequency for energies to log file and energy file
22nstlog                   = 100
23nstenergy                = 5000
24; Output frequency and precision for xtc file
25nstxout-compressed       = 100
26compressed-x-precision   = 1000
27; Selection of energy groups
28energygrps               = A  B
29
30; NEIGHBORSEARCHING PARAMETERS
31; nblist update frequency
32nstlist                  = 5
33; ns algorithm (simple or grid)
34ns-type                  = Grid
35; Periodic boundary conditions: xyz, no, xy
36pbc                      = xyz
37periodic_molecules       = no
38; nblist cut-off
39rlist                    = 1.4
40
41; OPTIONS FOR ELECTROSTATICS AND VDW
42; Method for doing electrostatics
43coulombtype              = User
44rcoulomb-switch          = 0
45rcoulomb                 = 1.4
46; Relative dielectric constant for the medium and the reaction field
47epsilon_r                = 1
48epsilon_rf               = 80
49; Method for doing Van der Waals
50vdw-type                 = User
51; cut-off lengths
52rvdw-switch              = 0
53rvdw                     = 1.4
54; Apply long range dispersion corrections for Energy and Pressure
55DispCorr                 = EnerPres
56; Extension of the potential lookup tables beyond the cut-off
57table-extension          = 1
58; Seperate tables between energy group pairs
59energygrp_table          = A  A  B   B   A  B
60; Spacing for the PME/PPPM FFT grid
61fourierspacing           = 0.12
62; FFT grid size, when a value is 0 fourierspacing will be used
63fourier_nx               = 0
64fourier_ny               = 0
65fourier_nz               = 0
66; EWALD/PME/PPPM parameters
67pme_order                = 4
68ewald_rtol               = 1e-05
69ewald_geometry           = 3d
70epsilon_surface          = 0
71
72; IMPLICIT B  VENT ALGORITHM
73implicit_solvent         = No
74
75; GENERALIZED BORN ELECTROSTATICS
76; Algorithm for calculating Born radii
77gb_algorithm             = Still
78; Frequency of calculating the Born radii inside rlist
79nstgbradii               = 1
80; Cutoff for Born radii calculation; the contribution from atoms
81; between rlist and rgbradii is updated every nstlist steps
82rgbradii                 = 2
83; Dielectric coefficient of the implicit solvent
84gb_epsilon_solvent       = 80
85; Salt concentration in M for Generalized Born models
86gb_saltconc              = 0
87; Scaling factors used in the OBC GB model. Default values are OBC(II)
88gb_obc_alpha             = 1
89gb_obc_beta              = 0.8
90gb_obc_gamma             = 4.85
91; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
92; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
93sa_surface_tension       = 2.092
94
95; OPTIONS FOR WEAK COUPLING ALGORITHMS
96; Temperature coupling
97Tcoupl                   = no
98; Groups to couple separately
99tc-grps                  = System
100; Time constant (ps) and reference temperature (K)
101tau_t                    = 0.2
102ref_t                    = 300
103; Pressure coupling
104Pcoupl                   = no
105Pcoupltype               = isotropic
106; Time constant (ps), compressibility (1/bar) and reference P (bar)
107tau_p                    = 0.5
108compressibility          = 4.5e-5
109ref_p                    = 1.0
110; Scaling of reference coordinates, No, All or COM
111refcoord_scaling         = No
112
113; GENERATE VELOCITIES FOR STARTUP RUN
114gen-vel                  = no
115
116; OPTIONS FOR BONDS
117constraints              = none
118