; Output control
nstxout = 0 ; save coordinates every 1.0 ps
nstvout = 0 ; save velocities every 1.0 ps
nstenergy = 100000 ; save energies every 1.0 ps
nstlog = 100000 ; update log file every 1.0 ps
; Bond parameters
continuation = yes ; Restarting after NVT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres ; account for cut-off vdW scheme
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = system ; coupling groups
tau_t = 0.1 ; time constant, in ps
ref_t = 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = semiisotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 1.0 ; reference pressure, in bar
compressibility = 0 4.5e-5 ; isothermal compressibility of water, bar^-1
refcoord_scaling = com