Fatal error:
Step 0: The total potential energy is 2.01494e+17, which is extremely high.
The LJ and electrostatic contributions to the energy are 2.01494e+17 and
-3.41276e+06, respectively. A very high potential energy can be caused by
overlapping interactions in bonded interactions or very large coordinate
values. Usually this is caused by a badly- or non-equilibrated initial
configuration, incorrect interactions or parameters in the topology.
nvt平衡的mdp文件：
; GROMOS 54A7 force field
integrator = md ; leap-frog integrator
nsteps = 125000 ; 2 * 125000 = 250 ps
dt = 0.002 ; 2 fs
comm-mode = Linear ; remove translational motion of COM
nstcomm = 100 ; remove every 100 steps
; Output control
nstxout = 0 ; do not save full precision coordinates
nstxout-compressed = 1000 ; write compressed coordinates every 2.0 ps
nstvout = 0 ; save velocities every 2.0 ps
nstenergy = 1000 ; save energies every 2.0 ps
nstlog = 1000 ; update log file every 2.0 ps
; Bond constraints
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighbour searching
cutoff-scheme = Verlet
nstlist = 10 ; frequency to update neighbour list (ps)
rlist = 1.4 ; short-range neighbourlist cutoff (nm)
; van der Waals
vdwtype = cutoff ; cut off vdw after rvdw (don't scale or shift)
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
DispCorr = no ; do not account for cut-off vdW scheme
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Water_and_ions ; two coupling groups
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 298 298 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Velocity generation
continuation = no ; first dynamics run
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 50 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
; Simulated annealing to heat system from 50 to 298 K
annealing = single single
annealing_npoints = 3 3
annealing_time = 0 10 210 0 10 210
annealing_temp = 50 50 298 50 50 298