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Hello,
While I am running an npt equilibration, the following message appears and the run stopped.
“Step 800 Warning: pressure scaling more than 1%, mu: 0.9334 0.9334 0.9334
Segmentation fault (core dumped)”
the npt.mdp file settings:
title = NPT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 2500000 ; 2 * 2500000 = 5000 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 500 ; save coordinates every 1.0 ps
nstvout = 500 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
; Bond parameters
continuation = yes ; Restarting after NVT
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
vdwtype = cutoff
vdw-modifier = force-switch
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rvdw-switch = 1.0 ; short-range van der Waals cutoff (in nm)
rvdw = 1.2
rlist = 1.4
dispcorr = no
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = System
tau_t = 1.0
ref_t = 300
; Pressure coupling is on
pcoupl = C-rescale
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 5.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = no ; Velocity generation is off
How to resolve the issue. Thank you