I have concern about the comment of gromacs output that energy minimization reached the maximum number of steps before the forces reached the requested precision.
Here's the output of minimization:
"Steepest Descents:
Tolerance (Fmax) = 1.00000e+01
Number of steps = 5000
Energy minimization reached the maximum number of steps before the forces
reached the requested precision Fmax < 10.
The result is fine. You'll likely never converge to emtol < 10 for most systems.
Thank you Justin.
I did equilibration after the minimization as I mentioned above in scripts but system crashed with following error message.
"Atom 22070 moved more than the distance allowed by the domain decomposition (11618422358016.000000) in direction Z
distance out of cell 11377049600.000000
New coordinates: 5207475355648.000 37863047561216.000 11629799407616.000
Old cell boundaries in direction Z: 0.000 4.845
New cell boundaries in direction Z: 0.000 11618422358016.000
Program: gmx mdrun, version 2019.1
Source file: src/gromacs/domdec/redistribute.cpp (line 250)
MPI rank: 2 (out of 4)
Fatal error:
One or more atoms moved too far between two domain decomposition steps.
This usually means that your system is not well equilibrated"
Here is the .mdp file
define = -DDUMMY_POS_RES
integrator = md
tinit = 0.0
dt = 0.020
nsteps = 5000000
nstxout = 50000
nstvout = 50000
nstfout = 50000
nstlog = 50000
nstenergy = 50000
nstxout-compressed = 5000
compressed-x-precision = 100
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
epsilon_r = 15
coulombtype = reaction-field
rcoulomb = 1.1
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1
tcoupl = v-rescale
tc-grps = system
tau_t = 1.0
ref_t = 303.15
; Pressure coupling:
Pcoupl = berendsen
Pcoupltype = semiisotropic
tau_p = 12.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel = no
refcoord_scaling = all
I'd equilibrate in NVT first and then NPT second, which is the suggested protocol (pcoupl section). Second issue I see is to use refcoord_scaling = com instead.
Also, if you search "blowing up" gromacs I believe there is a trouble shooting section in the manual.
I did NVT and NPT equilibration , I am still getting similar error. Unfortunately, the distribution of solvent [martini water] is inhomogeneous in the box.
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