1 title       = OPLS Lysozyme NPT equilibration
 2 define      = -DPOSRES  ; position restrain the protein
 3 ; Run parameters
 4 integrator  = md        ; leap-frog integrator
 5 nsteps      = 50000     ; 2 * 50000 = 100 ps
 6 dt          = 0.002     ; 2 fs
 7 ; Output control
 8 nstxout     = 500       ; save coordinates every 1.0 ps
 9 nstvout     = 500       ; save velocities every 1.0 ps
10 nstenergy   = 500       ; save energies every 1.0 ps
11 nstlog      = 500       ; update log file every 1.0 ps
12 ; Bond parameters
13 continuation            = yes       ; Restarting after NVT
14 constraint_algorithm    = lincs     ; holonomic constraints
15 constraints             = all-bonds ; all bonds (even heavy atom-H bonds) constrained
16 lincs_iter              = 1         ; accuracy of LINCS
17 lincs_order             = 4         ; also related to accuracy
18 ; Neighborsearching
19 cutoff-scheme   = Verlet
20 ns_type         = grid      ; search neighboring grid cells
21 nstlist         = 10        ; 20 fs, largely irrelevant with Verlet scheme
22 rcoulomb        = 1.0       ; short-range electrostatic cutoff (in nm)
23 rvdw            = 1.0       ; short-range van der Waals cutoff (in nm)
24 ; Electrostatics
25 coulombtype     = PME       ; Particle Mesh Ewald for long-range electrostatics
26 pme_order       = 4         ; cubic interpolation
27 fourierspacing  = 0.16      ; grid spacing for FFT
28 ; Temperature coupling is on
29 tcoupl      = V-rescale             ; modified Berendsen thermostat
30 tc-grps     = Protein Non-Protein   ; two coupling groups - more accurate
31 tau_t       = 0.1     0.1           ; time constant, in ps
32 ref_t       = 300     300           ; reference temperature, one for each group, in K
33 ; Pressure coupling is on
34 pcoupl              = Parrinello-Rahman     ; Pressure coupling on in NPT
35 pcoupltype          = isotropic             ; uniform scaling of box vectors
36 tau_p               = 2.0                   ; time constant, in ps
37 ref_p               = 1.0                   ; reference pressure, in bar
38 compressibility     = 4.5e-5                ; isothermal compressibility of water, bar^-1
39 refcoord_scaling    = com
40 ; Periodic boundary conditions
41 pbc     = xyz       ; 3-D PBC
42 ; Dispersion correction
43 DispCorr    = EnerPres  ; account for cut-off vdW scheme
44 ; Velocity generation
45 gen_vel     = no        ; Velocity generation is off