1;
2;	File 'mdout.mdp' was generated
3;	By user: mark (1302)
4;	On host: amd2
5;	At date: Wed Dec 19 13:44:25 2012
6;
7
8; VARIOUS PREPROCESSING OPTIONS
9; Preprocessor information: use cpp syntax.
10; e.g.: -I/home/joe/doe -I/home/mary/roe
11include                  =
12; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
13define                   = -DPOSRES
14
15; RUN CONTROL PARAMETERS
16integrator               = md
17; Start time and timestep in ps
18tinit                    = 0.0
19dt                       = 0.001
20nsteps                   = 20
21; For exact run continuation or redoing part of a run
22init-step                = 0
23; Part index is updated automatically on checkpointing (keeps files separate)
24simulation-part          = 1
25
26; OUTPUT CONTROL OPTIONS
27; Output frequency for coords (x), velocities (v) and forces (f)
28nstxout                  = 20
29nstvout                  = 20
30nstfout                  = 20
31; Output frequency for energies to log file and energy file
32nstlog                   = 20
33nstcalcenergy            = 1
34nstenergy                = 1
35
36; NEIGHBORSEARCHING PARAMETERS
37; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs)
38cutoff-scheme            = Verlet
39; nblist update frequency
40nstlist                  = 10
41; Periodic boundary conditions: xyz, no, xy
42pbc                      = xyz
43periodic-molecules       = no
44; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom,
45; a value of -1 means: use rlist
46verlet-buffer-tolerance      = 0.005
47; nblist cut-off
48rlist                    = 1.0
49
50; OPTIONS FOR ELECTROSTATICS AND VDW
51; Method for doing electrostatics
52coulomb_type             = pme
53coulomb-modifier         = Potential-shift-Verlet
54rcoulomb_switch          = 0.99
55rcoulomb                 = 1.0
56; Relative dielectric constant for the medium and the reaction field
57epsilon_r                = 1.0
58epsilon-rf               = 0
59; Method for doing Van der Waals
60vdw_type                 = Cut-off
61vdw-modifier             = Force-switch
62; cut-off lengths
63rvdw_switch              = 0.8
64rvdw                     = 1
65; Apply long range dispersion corrections for Energy and Pressure
66dispcorr                 = enerpres
67; Extension of the potential lookup tables beyond the cut-off
68table-extension          = 1
69; Seperate tables between energy group pairs
70energygrp-table          =
71; Spacing for the PME/PPPM FFT grid
72fourierspacing           = 0.12
73
74; EWALD/PME/PPPM parameters
75pme-order                = 4
76ewald_rtol               = 1e-6
77ewald-geometry           = 3d
78epsilon-surface          = 0
79
80; OPTIONS FOR WEAK COUPLING ALGORITHMS
81; Temperature coupling
82tcoupl                   = berendsen
83nsttcouple               = 1
84; Groups to couple separately
85tc-grps                  = system
86; Time constant (ps) and reference temperature (K)
87tau_t                    = 1.0
88ref_t                    = 298
89; pressure coupling
90Pcoupl                   = no
91
92; GENERATE VELOCITIES FOR STARTUP RUN
93gen-vel                  = no
94
95; OPTIONS FOR BONDS
96constraints              = h-bonds
97; Type of constraint algorithm
98constraint-algorithm     = Lincs
99; Do not constrain the start configuration
100continuation             = no
101; Highest order in the expansion of the constraint coupling matrix
102lincs-order              = 8
103; Number of iterations in the final step of LINCS. 1 is fine for
104; normal simulations, but use 2 to conserve energy in NVE runs.
105; For energy minimization with constraints it should be 4 to 8.
106lincs-iter               = 2
107; Lincs will write a warning to the stderr if in one step a bond
108; rotates over more degrees than
109lincs-warnangle          = 30
110; Convert harmonic bonds to morse potentials
111morse                    = no
112
113; ENERGY GROUP EXCLUSIONS
114; Pairs of energy groups for which all non-bonded interactions are excluded
115energygrp-excl           =
116
117; Free energy variables
118free-energy              = yes
119couple_moltype           =
120couple_lambda0           = vdw-q
121couple_lambda1           = vdw-q
122init-lambda-state        = 12
123nstdhdl                  = 5
124fep-lambdas              = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.0
125mass-lambdas             =
126coul-lambdas             = 0.0 0.1 0.2 0.3 0.5 0.7 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.0
127vdw-lambdas              = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 1.0
128bonded-lambdas           = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 1.0
129restraint-lambdas        = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 0.9 0.9 0.9 0.90 0.9 1.00 1.0 1.00 1.0 1.0
130temperature-lambdas      =
131init-lambda-weights      =
132dhdl-print-energy        = no
133sc-alpha                 = 0.5
134sc-power                 = 1
135sc-r-power               = 6
136sc-sigma                 = 0.3
137sc-coul                  = no
138separate-dhdl-file       = no
139dhdl-derivatives         = yes
140dh_hist_size             = 0
141dh_hist_spacing          = 0.1
142
143