Unfortunately I closed the terminal window but here is the last part of my .log file for NVT calculation:

Input Parameters:

integrator = md

tinit = 0

dt = 0.002

nsteps = 100000

init-step = 0

simulation-part = 1

comm-mode = Linear

nstcomm = 100

bd-fric = 0

ld-seed = 267344549

emtol = 10

emstep = 0.01

niter = 20

fcstep = 0

nstcgsteep = 1000

nbfgscorr = 10

rtpi = 0.05

nstxout = 500

nstvout = 500

nstfout = 0

nstlog = 500

nstcalcenergy = 100

nstenergy = 500

nstxout-compressed = 0

compressed-x-precision = 1000

cutoff-scheme = Verlet

nstlist = 10

pbc = xyz

periodic-molecules = false

verlet-buffer-tolerance = 0.005

rlist = 1.378

coulombtype = Cut-off

coulomb-modifier = Potential-shift

rcoulomb-switch = 0

rcoulomb = 1.3

epsilon-r = 1

epsilon-rf = inf

vdw-type = Cut-off

vdw-modifier = Potential-shift

rvdw-switch = 0

rvdw = 1.3

DispCorr = No

table-extension = 1

fourierspacing = 0.12

fourier-nx = 0

fourier-ny = 0

fourier-nz = 0

pme-order = 4

ewald-rtol = 1e-05

ewald-rtol-lj = 0.001

lj-pme-comb-rule = Geometric

ewald-geometry = 0

epsilon-surface = 0

tcoupl = V-rescale

nsttcouple = 10

nh-chain-length = 0

print-nose-hoover-chain-variables = false

pcoupl = No

pcoupltype = Isotropic

nstpcouple = -1

tau-p = 1

compressibility (3x3):

compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}

compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}

compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}

ref-p (3x3):

ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}

ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}

ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}

refcoord-scaling = No

posres-com (3):

posres-com[0]= 0.00000e+00

posres-com[1]= 0.00000e+00

posres-com[2]= 0.00000e+00

posres-comB (3):

posres-comB[0]= 0.00000e+00

posres-comB[1]= 0.00000e+00

posres-comB[2]= 0.00000e+00

QMMM = false

QMconstraints = 0

QMMMscheme = 0

MMChargeScaleFactor = 1

qm-opts:

ngQM = 0

constraint-algorithm = Lincs

continuation = false

Shake-SOR = false

shake-tol = 0.0001

lincs-order = 4

lincs-iter = 1

lincs-warnangle = 30

nwall = 0

wall-type = 9-3

wall-r-linpot = -1

wall-atomtype[0] = -1

wall-atomtype[1] = -1

wall-density[0] = 0

wall-density[1] = 0

wall-ewald-zfac = 3

pull = false

awh = false

rotation = false

interactiveMD = false

disre = No

disre-weighting = Conservative

disre-mixed = false

dr-fc = 1000

dr-tau = 0

nstdisreout = 100

orire-fc = 0

orire-tau = 0

nstorireout = 100

free-energy = no

cos-acceleration = 0

deform (3x3):

deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}

deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}

deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}

simulated-tempering = false

swapcoords = no

userint1 = 0

userint2 = 0

userint3 = 0

userint4 = 0

userreal1 = 0

userreal2 = 0

userreal3 = 0

userreal4 = 0

applied-forces:

electric-field:

x:

E0 = 0

omega = 0

t0 = 0

sigma = 0

y:

E0 = 0

omega = 0

t0 = 0

sigma = 0

z:

E0 = 0

omega = 0

t0 = 0

sigma = 0

density-guided-simulation:

active = false

group = protein

similarity-measure = inner-product

atom-spreading-weight = unity

force-constant = 1e+09

gaussian-transform-spreading-width = 0.2

gaussian-transform-spreading-range-in-multiples-of-width = 4

reference-density-filename = reference.mrc

nst = 1

normalize-densities = true

adaptive-force-scaling = false

adaptive-force-scaling-time-constant = 4

grpopts:

nrdf: 17997

ref-t: 300

tau-t: 0.1

annealing: No

annealing-npoints: 0

acc: 0 0 0

nfreeze: N N N

energygrp-flags[ 0]: 0

Changing nstlist from 10 to 25, rlist from 1.378 to 1.548

Using 1 MPI thread

Non-default thread affinity set, disabling internal thread affinity

Using 8 OpenMP threads

System total charge: 0.000

Potential shift: LJ r^-12: -4.292e-02 r^-6: -2.072e-01, Coulomb -8e-01

Generated table with 1273 data points for 1-4 COUL.

Tabscale = 500 points/nm

Generated table with 1273 data points for 1-4 LJ6.

Tabscale = 500 points/nm

Generated table with 1273 data points for 1-4 LJ12.

Tabscale = 500 points/nm

Using SIMD 4x8 nonbonded short-range kernels

Using a dual 4x8 pair-list setup updated with dynamic pruning:

outer list: updated every 25 steps, buffer 0.248 nm, rlist 1.548 nm

inner list: updated every 4 steps, buffer 0.021 nm, rlist 1.321 nm

At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:

outer list: updated every 25 steps, buffer 0.322 nm, rlist 1.622 nm

inner list: updated every 4 steps, buffer 0.030 nm, rlist 1.330 nm

Using Lorentz-Berthelot Lennard-Jones combination rule

Removing pbc first time

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++

G. Bussi, D. Donadio and M. Parrinello

Canonical sampling through velocity rescaling

J. Chem. Phys. 126 (2007) pp. 014101

-------- -------- — Thank You — -------- --------

There are: 6000 Atoms

Center of mass motion removal mode is Linear

We have the following groups for center of mass motion removal:

0: rest

Initial temperature: 297.989 K

Started mdrun on rank 0 Wed Sep 13 23:49:04 2023

```
Step Time
0 0.00000
```

Energies (kJ/mol)

Bond Angle Proper Dih. LJ-14 Coulomb-14

1.65121e+02 1.78406e+03 1.01411e+03 -8.17716e+02 -5.48976e+04

LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy

-9.65450e+03 -3.29584e+03 -6.57024e+04 4.52880e+04 -2.04144e+04

Conserved En. Temperature Pressure (bar)

-2.04144e+04 6.05311e+02 7.87726e+03