cool_NPT.mdp

;
; ****  Gromacs run parameters for OPLS-AA simulations  ****
;
; **** NPT equilibration
; 
; References:
; - S. Riniker, J. Chem. Inf. Model. 2018, DOI: 10.1021/acs.jcim.8b00042
; - L.S. Dodda, et al., Nucleic Acids Res. 2017, DOI: 10.1093/nar/gkx312
; - C. Caleman, et al., J. Chem. Theory. Comput. 2021, DOI: 10.1021/ct200731v 
;

; Integrator
integrator               = md
dt                       = 0.001             ; 1 fs
nsteps                  = 85000000           ; 1 ns
constraint_algorithm     = lincs             ; default
constraints              = h-bonds           ; constrain bonds involving hydrogens
lincs_order              = 4                 ; default

; Output Control
nstxout                  = 500000            ; pos out   ---  1000  ps
nstvout                  = 500000            ; vel out   ---  1000  ps
nstfout                  = 0                 ; force out ---  no
nstlog                   = 10000             ; energies to log (20 ps)
nstenergy                = 10000             ; energies to energy file
energygrps               = System
nstxtcout                = 10000             ; xtc, 10 ps
compressed-x-precision   = 1000              ; default is 1000

; Some specific settings
pbc                      = xyz
periodic_molecules       = no                ; default
comm_mode                = Linear

; Neighboring search and cutoff scheme
cutoff-scheme            = Verlet
nstlist                  = 10                ; default
ns-type                  = grid
rlist                    = 1.1               ; ignored with Verlet

; Coulombic
coulombtype              = PME
rcoulomb                 = 1.1   
fourierspacing           = 0.12              ; default

; VDW
vdwtype                  = cut-off
rvdw                     = 1.1    
DispCorr                 = EnerPres          ; long-range correction

; Temperature Coupling
tcoupl                   = v-rescale
tc-grps                  = system
tau-t                    = 0.1               ; ps
ref_t                    = 900            ; sets the temperature 

; Pressure Coupling
Pcoupl                   = berendsen 
Pcoupltype               = isotropic        
ref_p                    = 1.0               ; bar
compressibility          = 5e-5              ; 1/bar
tau_p                    = 0.5               ; ps
refcoord_scaling         = all

; Generate velocites in the beginning
gen_vel                  = no 
gen_temp                 = 298.15
gen_seed                 = -1                ; -1 = the seed is calculated from the process ID number

; Ensure smooth continuation
continuation             = yes
                                 
; Cool down the system
annealing                = single
annealing-npoints        = 3
annealing-time           =   0 5000 85000 ; cooling rate 10Kns
annealing-temp           = 900  900     100 ; cooling rate 10Kns