GROMACS version: 2021.2
GROMACS modification: No
I’m simulating protein in water using CHARMM27 and tip4p water type
I’ve got this error message during nvt equilibration:
Fatal error:
Step 0: The total potential energy is 2.50582e+18, which is extremely high.
The LJ and electrostatic contributions to the energy are 2.50582e+18 and
47863.9, 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.
here my nvt.mdp file
title = NVT equilibration
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 500000 ; 2 * 50000 = 1000 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 5000 ; save coordinates every 1.0 ps
nstvout = 5000 ; save velocities every 1.0 ps
nstenergy = 5000 ; save energies every 1.0 ps
nstlog = 5000 ; update log file every 1.0 ps
nstxout-compressed = 5000 ; save compressed coordinates every 1.0 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres ; account for cut-off vdW scheme
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
~