title = NPT Ensemble Annealing step - 1
;Integrator
integrator = md ; leap-frog integrator
dt = 0.002 ; timestep (pfs)
nsteps = 5000000 ; 10 ns
comm-mode = Linear
; OUTPUT CONTROL OPTIONS
nstxtcout = 0 ; compressed co-ordinates
nstlog = 50000 ; freq. energies/lincs deviation to log file 10 ps
nstenergy = 5000 ; freq. to write energy to .edr every 10 ps
nstxout = 50000 ; full precision, r, every 50ps
nstvout = 50000 ; full precision, v, every 50ps
nstfout = 50000 ; full precision, f, every 50ps
xtc-precision = 1000
xtc-grps = System
energygrps = System
; NEIGHBORSEARCHING PARAMETERS
nstlist = 10
ns_type = grid
pbc = xyz
; OPTIONS FOR ELECTROSTATICS AND VDW
cutoff-scheme = Verlet
; rlist is not needed as it is dynamically updated according to verlet-buffer-drift/verlet scheme
coulombtype = PME
rcoulomb = 1.0
;shift vdw potential to zero at cut-off with verlet scheme
vdw-type = Cut-off
rvdw = 1.0
; Temperature coupling
tcoupl = V-rescale ; V-rescale Thermostat
tc-grps = System
tau-t = 0.1 ; coupling time constant [ps]
ref-t = 300 ; reference coupling temperature [K]
; Pressure coupling
pcoupl = Berendsen ;Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel = no ; use velocity from previous step
; OPTIONS FOR BONDS
constraints = h-bonds ; h-bonds are converted to constraints
constraint-algorithm = Lincs
; Do not apply constraints to starting confirmation (before first step)
continuation = yes
lincs-order = 4
lincs-iter = 2
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme