GROMACS version: 2022
GROMACS modification: NoHi every one.
I have this system, jannus MoSSe, with nanopore passivated with H atoms. I generated my force field files via acpype.
I tried, many times, to simulation my system but I had one specific issue:
”Steepest Descents converged to machine precision in 4919 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 8.0552238e+05
Maximum force = 1.1924229e+04 on atom 730
Norm of force = 4.1685461e+02”
So, the system not converge and I tried using:
integrator = steep
nsteps = 50000
; EM criteria and other stuff
emtol = 1000
emstep = 0.01
niter = 20
Change the emstep from 0.1 to 0.01 and nothing worked. I tried too understanding what happened with the atom 730 (which means a H) and this specific atom has the same distance to others H atoms in my system. Anyone can help?
this my 1-EM.mdp:
integrator = steep
nsteps = 50000
; EM criteria and other stuff
emtol = 1000
emstep = 0.01
niter = 20
nbfgscorr = 10
; Output control
nstlog = 1
nstenergy = 1
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme = verlet
nstlist = 20 ; 1
ns_type = grid
pbc = xyz
rlist = 1.2
;PBC
periodic-molecules = yes
; Electrostatics
coulombtype = PME
rcoulomb = 1.2
; van der Waals
vdwtype = cutoff
vdw-modifier = potential-switch
rvdw-switch = 1.0
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
optimize_fft = yes
; EWALD/PME/PPPM parameters
pme_order = 6
ewald_rtol = 1e-06
epsilon_surface = 0
; Temperature and pressure coupling are off during EM
tcoupl = no
pcoupl = no
; No velocities during EM
gen_vel = no
; options for bonds
constraints = h-bonds ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Do not constrain the starting configuration
continuation = no
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 12
freezegrps = MEMB ;SOL
freezedim = Y Y Y;N N N
;Y Y N N N N means that particles in the first group can move only in Z direction.
I need to keep my membrane fixed, but my H its allowed to move in the system.