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"

Can you provide your .mdp file?

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.

^I've never used martini water so maybe somebody else can chime in. However, if it helps at all, I typically also turn down the position restraints for my larger systems. So, when I equilibrate, I do a first step in NVT with strong position restraints on anything but solvent and ions. In my case,

- I start with force constants of 1000 in NVT on DNA+protein ->

- my custom (lower) fc in NVT on protein + DNA ->

-NPT at low fc.

You could try stronger restraints on your non-solvent system first.