1; VARIOUS PREPROCESSING OPTIONS
2; Preprocessor - specify a full path if necessary.
3include                  =
4define                   =
5
6; RUN CONTROL PARAMETERS
7integrator               = sd
8; Start time and timestep in ps
9tinit                    = 0
10dt                       = 0.001
11nsteps                   = 100000
12; For exact run continuation or redoing part of a run
13init_step                = 0
14; mode for center of mass motion removal
15comm-mode                = Linear
16; number of steps for center of mass motion removal
17nstcomm                  = 10
18; group(s) for center of mass motion removal
19comm_grps                =
20;system
21
22; LANGEVIN DYNAMICS OPTIONS
23; Friction coefficient (amu/ps) and random seed
24ld-seed                  = 1993
25
26; OUTPUT CONTROL OPTIONS
27; Output frequency for coords (x), velocities (v) and forces (f)
28nstxout                  = 0
29nstvout                  = 0
30nstfout                  = 0
31; Output frequency for energies to log file and energy file
32nstlog                   = 100
33nstenergy                = 100
34; Output frequency and precision for xtc file
35nstxout-compressed       = 100
36compressed-x-precision   = 1000
37; This selects the subset of atoms for the xtc file. You can
38; select multiple groups. By default all atoms will be written.
39compressed-x-grps        = System ;Protein
40; Selection of energy groups
41energygrps               = A B
42
43; NEIGHBORSEARCHING PARAMETERS
44; nblist update frequency
45nstlist                  = 10
46; ns algorithm (simple or grid)
47ns_type                  = grid
48; Periodic boundary conditions: xyz (default), no (vacuum)
49; or full (infinite systems only)
50pbc                      = xyz
51; nblist cut-off
52rlist                    = 1.5
53
54
55; OPTIONS FOR ELECTROSTATICS AND VDW
56; Method for doing electrostatics
57coulombtype              = Cut-off
58rcoulomb-switch          = 0
59rcoulomb                 = 1.5
60; Relative dielectric constant for the medium and the reaction field
61epsilon_r                = 1
62epsilon_rf               = 1
63; Method for doing Van der Waals
64vdwtype                  = user
65; cut-off lengths
66rvdw-switch              = 0
67rvdw                     = 1.5
68; Apply long range dispersion corrections for Energy and Pressure
69DispCorr                 = EnerPres
70; Extension of the potential lookup tables beyond the cut-off
71table-extension          = 1.0
72; Seperate tables between energy group pairs
73energygrp_table          = A A B B A B
74; Spacing for the PME/PPPM FFT grid
75fourierspacing           = 0.12
76; FFT grid size, when a value is 0 fourierspacing will be used
77fourier_nx               = 0
78fourier_ny               = 0
79fourier_nz               = 0
80; EWALD/PME/PPPM parameters
81pme_order                = 4
82ewald_rtol               = 1e-05
83ewald_geometry           = 3d
84epsilon_surface          = 0
85
86; OPTIONS FOR WEAK COUPLING ALGORITHMS
87; Temperature coupling
88tcoupl                   = no
89; Groups to couple separately
90tc-grps                  = System
91; Time constant (ps) and reference temperature (K)
92tau_t                    = 1.0
93ref_t                    = 300
94; Pressure coupling
95Pcoupl                   = no
96pcoupltype               = isotropic
97; Time constant (ps), compressibility (1/bar) and reference P (bar)
98tau_p                    = 0.5
99compressibility          = 4.5e-5
100ref_p                    = 1.0
101
102
103; GENERATE VELOCITIES FOR STARTUP RUN
104gen_vel                  = yes
105gen_temp                 = 300
106gen_seed                 = -1
107
108; OPTIONS FOR BONDS
109constraints              = none
110; Type of constraint algorithm
111constraint_algorithm     = LINCS
112; Use successive overrelaxation to reduce the number of shake iterations
113Shake-SOR                = no
114; Relative tolerance of shake
115shake-tol                = 1e-04
116; Highest order in the expansion of the constraint coupling matrix
117lincs-order              = 4
118; Number of iterations in the final step of LINCS. 1 is fine for
119; normal simulations, but use 2 to conserve energy in NVE runs.
120; For energy minimization with constraints it should be 4 to 8.
121lincs_iter               = 2
122; Lincs will write a warning to the stderr if in one step a bond
123; rotates over more degrees than
124lincs-warnangle          = 30
125; Convert harmonic bonds to morse potentials
126morse                    = no
127
128; ENERGY GROUP EXCLUSIONS
129; Pairs of energy groups for which all non-bonded interactions are excluded
130energygrp_excl           =
131
132