1; RUN CONTROL PARAMETERS
2integrator               = sd
3; Start time and timestep in ps
4tinit                    = 0
5dt                       = 0.002
6nsteps                   = 100000
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 forces (f)
18nstxout                  = 200
19nstvout                  = 0
20nstfout                  = 200
21; Output frequency for energies to log file and energy file
22nstlog                   = 0
23nstenergy                = 200
24; Output frequency and precision for xtc file
25nstxout-compressed       = 200
26compressed-x-precision   = 1000
27; Selection of energy groups
28energygrps               = LJ1 LJ2
29
30; NEIGHBORSEARCHING PARAMETERS
31; nblist update frequency
32nstlist                  = 10
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                    = 1.2
40
41; OPTIONS FOR ELECTROSTATICS AND VDW
42; Method for doing electrostatics
43coulombtype              = Reaction-Field
44rcoulomb-switch          = 0
45rcoulomb                 = 1.2
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                     = 1.2
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          = LJ1 LJ1 LJ1 LJ2 LJ2 LJ2
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 SOLVENT ALGORITHM
73implicit_solvent         = No
74
75
76; OPTIONS FOR WEAK COUPLING ALGORITHMS
77; Temperature coupling
78Tcoupl                   = no
79; Groups to couple separately
80tc-grps                  = System
81; Time constant (ps) and reference temperature (K)
82tau_t                    = 0.5
83ref_t                    = 85
84; Pressure coupling
85Pcoupl = No
86;Pcoupl                   = Parrinello-Rahman
87Pcoupltype               = isotropic
88; Time constant (ps), compressibility (1/bar) and reference P (bar)
89tau_p                    = 0.5
90compressibility          = 4.5e-5
91ref_p                    = 1.0
92; Scaling of reference coordinates, No, All or COM
93refcoord_scaling         = No
94
95; GENERATE VELOCITIES FOR STARTUP RUN
96gen-vel                  = no
97
98; OPTIONS FOR BONDS
99constraints              = none
100