GROMACS version:2024.4
GROMACS modification: No
Hello! I left my computer to run md last night, but today I found my computer power off. This is my .log file, it seems not finished? If it is possible to start from where it stopped?
the tail of .log file reads like this:
Step Time
3095000 6190.00000
Energies (kJ/mol)
U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
1.73558e+04 2.02103e+04 1.13603e+03 -1.10442e+03 7.75147e+03
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
9.13033e+04 1.96153e+05 -1.18033e+04 -2.34625e+06 6.69117e+03
Potential Kinetic En. Total Energy Conserved En. Temperature
-2.01856e+06 3.71626e+05 -1.64693e+06 -1.95129e+06 2.98796e+02
Pres. DC (bar) Pressure (bar) Constr. rmsd
-1.34298e+02 -1.75921e+02 3.41630e-05
And the input parameters are these:
Input Parameters:
integrator = md
tinit = 0
dt = 0.002
nsteps = 5000000
init-step = 0
simulation-part = 1
mts = false
mass-repartition-factor = 1
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = -274744321
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 5000
nstcalcenergy = 100
nstenergy = 5000
nstxout-compressed = 10000
compressed-x-precision = 1000
cutoff-scheme = Verlet
nstlist = 10
pbc = xyz
periodic-molecules = false
verlet-buffer-tolerance = 0.005
verlet-buffer-pressure-tolerance = 0.5
rlist = 1.2
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 1.2
epsilon-r = 1
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 1.2
DispCorr = EnerPres
table-extension = 1
fourierspacing = 0.16
fourier-nx = 80
fourier-ny = 80
fourier-nz = 80
pme-order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
ensemble-temperature-setting = constant
ensemble-temperature = 298
tcoupl = Nose-Hoover
nsttcouple = 2
nh-chain-length = 1
print-nose-hoover-chain-variables = false
pcoupl = Parrinello-Rahman
pcoupltype = Isotropic
nstpcouple = 50
tau-p = 2
compressibility (3x3):
compressibility[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
compressibility[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
ref-p (3x3):
ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
refcoord-scaling = All
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
qm-opts:
ngQM = 0
constraint-algorithm = Lincs
continuation = true
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
shift-vector =
transformation-matrix =
qmmm-cp2k:
active = false
qmgroup = System
qmmethod = PBE
qmfilenames =
qmcharge = 0
qmmultiplicity = 1
colvars:
active = false
configfile =
seed = -1
grpopts:
nrdf: 299176
ref-t: 298
tau-t: 0.1
annealing: No
annealing-npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0
So based on this .log file, my simulation is not finished? By what means can I proceed?
Guys I solve this problem using the following command:
gmx mdrun -v -deffnm md_0_10 -cpi md_0_10.cpt