eq_step1_min.mdp

;
; ****  Gromacs run parameters for OPLS-AA simulations  ****
;
; **** Energy minimazation
; 
; 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               = steep             ; steepest descent E minimization
nsteps                  = 80000
emtol                    = 100               ; default 
constraint_algorithm     = lincs             ; default
constraints              = none
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              = cutoff
rcoulomb                 = 1.1   
fourierspacing           = 0.12              ; default

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

; Temperature Coupling
tcoupl                   = no

; Pressure Coupling
Pcoupl                   = no 

; Generate velocites in the beginning
gen_vel                  = yes               ; generate velocities anew 
gen_temp                 = 298.15
gen_seed                 = -1                ; -1 = the seed is calculated from the process ID number