GROMACS version: 2024
GROMACS modification: Yes/No
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after running: gmx mdrun -deffnm npt
I am also providing the .tpr and .mdp file for your reference
npt.mdp (2.5 KB)
Step 400 Warning: pressure scaling more than 1%, mu: 0.955868 0.955868 0.955868
Step 400 Warning: pressure scaling more than 1%, mu: 0.955868 0.955868 0.955868
Step 400 Warning: pressure scaling more than 1%, mu: 0.955868 0.955868 0.955868
Step 400 Warning: pressure scaling more than 1%, mu: 0.955868 0.955868 0.955868
Step 400 Warning: pressure scaling more than 1%, mu: 0.955868 0.955868 0.955868
Step 400 Warning: pressure scaling more than 1%, mu: 0.955868 0.955868 0.955868
Step 400 Warning: pressure scaling more than 1%, mu: 0.955868 0.955868 0.955868
Step 400 Warning: pressure scaling more than 1%, mu: 0.955868 0.955868 0.955868
Step 400 Warning: pressure scaling more than 1%, mu: 0.955868 0.955868 0.955868
Step 400 Warning: pressure scaling more than 1%, mu: 0.955868 0.955868 0.955868
Step 400 Warning: pressure scaling more than 1%, mu: 0.955868 0.955868 0.955868
Step 400 Warning: pressure scaling more than 1%, mu: 0.955868 0.955868 0.955868
Step 500:
The update group starting at atom 376871 moved more than the distance allowed by the domain decomposition (1.066984) in direction X
distance out of cell -0.103346
Old coordinates: 28.729 20.923 11.206
New coordinates: 28.729 20.923 11.206
Old cell boundaries in direction X: 21.874 23.241
New cell boundaries in direction X: 20.909 22.215
Program: gmx mdrun, version 2024.1
Source file: src/gromacs/domdec/redistribute.cpp (line 219)
MPI rank: 248 (out of 255)
npt.mdp
title = OPLS Lysozyme NPT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 250000 ; 2 * 250000 = 500 ps
dt = 0.001 ; 1 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
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; 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 on
pcoupl = C-rescale ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 1.0 ; 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