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eq_step2_NVT.mdp
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eq_step2_NVT.mdp
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;
; **** Gromacs run parameters for OPLS-AA simulations ****
;
; **** NVT 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 = 100000; 0.1 ns ; 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 = cutoff
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 = 298.15 ; sets the temperature
; 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