md1.mdp

; NPT PRODUCTION RUN PARAMETERS FILE (for 1 microsecond simulation)
;
; RUN CONTROL PARAMETERS
;
integrator           =  md         ; leap-frog integrator.
init_step            =  500000     ; [steps] step to initialize, continuation of previous NPT equilibration. 
dt                   =  0.002      ; [ps] step-size.
nsteps               = 500000000   ; [steps] number of steps (500000000*0.002 = 1000000 ps = 1000 ns = 1 microsecond).
;
; BONDS PARAMETERS
;
continuation        =  yes       ; restarting after NPT equilibration.
constraints         =  h-bonds   ; apply contraints to H-atoms.
constraint_algorithm =  LINCS    ; LINear Constraints solver algorithm.
lincs_order         =   4        ; accuracy for the algorithm.  
lincs_iter          =   1        ; number of iterative corrections.
;
; OUTPUT CONTROL
nstxout                      =  50000 ; save coordinates every 100.0 ps.
nstvout                      =  50000 ; save velocities every 100.0 ps
nstfout                      =  50000 ; save forces every 100.0 ps
nstlog                       =  50000 ; update log file every 100.0 ps.
nstenergy                    =  50000 ; save energies every 100.0 ps
nstxout-compressed           =  5000  ; save coordinates to XTC file every 10.0 ps.
compressed-x-precision       =  5000  ; precision for the XTC file.
;
; NEIGHBORSEARCHING PARAMETERS
cutoff-scheme       = Verlet   ; buffered neighbor searching
nstlist             =  10      ; [steps] freq. to update neighbor list.
ns_type             =  grid    ; search neighboring grid cells.
pbc                 =  xyz     ; periodic boundary conditions in all directions.
periodic_molecules  =  no      ; molecules do not couple to themselves through PBC conditions.
rlist               =  1.0     ; [nm] cut-off distance.
;
; ELECTROSTATICS AND VDW PARAMETERS
coulombtype         =  PME         ; fast smooth particle mesh ewald for long-range.
rcoulomb            =  1.0         ; [nm] cut-off distance electrostatics.
vdwtype             =  Cut-off     ; plain cutoff with pair list radius (rlist) and vdw cutoff (rvdw).
rvdw                =  1.0         ; [nm] cut-off distance van der waals.
DispCorr            = EnerPres     ; apply long range dispersion corrections for Energy and Pressure.
fourierspacing      =  0.12        ; [nm] grid spacing for FFT. 
pme_order           =  4           ; 4 equals cubic interpolation. 
optimize_fft        =  yes         ; calculated optimal fft plan for grid startup. good for long simulations. 
;
; TEMPERATURE COUPLING PARAMETERS
Tcoupl              = v-rescale                 ; Similar to Berendsen but ensures canonical ensemble.
tc-grps             = Protein   Water_and_ions  ; groups to couple. See file indices.ndx from make_ndx.
tau_t               = 0.1       0.1             ; [ps] time constant for coupling for each group.
ref_t               = 300       300             ; [k] reference temperature for coupling for each group
;
; PRESSURE COUPLING PARAMETERS
Pcoupl              = Parrinello-Rahman  ; Extended-ensemble pressure coupling where the box vectors are subject to an equation of motion.
Pcoupltype          = isotropic          ; uniform scaling of box vectors
tau_p               = 0.5                ; [ps] time constant for coupling.
compressibility     = 4.5e-5             ; [bat^-1] isothermal compressibility of water
ref_p               = 1                  ; [bar] reference pressure
;
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel        = no       ; assign velocities from Maxwell distribution
ld-seed        = -1       ; generate a presudo-random seed.