[gmx-users] NPT Equilibration error

[Ankita naithani]

Hi,

I am trying to run NPT equilibration on two separate systems both with
ligands present in the structure.

However, I got two different errors for both of these and these are below:

Fatal error: A charge group moved too far between two domain
decomposition steps.

Fatal error: 8 particles communicated to PME node 1 are more than 2/3
times the cut off out of the domain decomposition cell of their charge
group in dimension X.

My npt.mdp files looks like follows:

title           = NPT equilibration
define          = -DPOSRES      ; position restrain the protein
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 125000        ; 250 ps
dt              = 0.002         ; 2 fs
; Output control
nstxout         = 0             ; save coordinates every 5 ps
nstvout         = 0             ; save velocities every 5 ps
nstenergy       = 10            ; save energies every 5 ps
nstlog          = 1000          ; update log file every 5 ps
; Bond parameters
continuation    = yes           ; first dynamics run
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
; Neighborsearching
ns_type         = grid          ; search neighboring grid cells
nstlist         = 10            ; 50 fs
rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
rlistlong       = 1.0           ; long-range neighborlist cutoff (in nm)
; 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          = berendsen     ; Berendsen thermostat
tc-grps         = Protein Non-Protein   ; two coupling groups - more accurate
tau_t           = 0.1   0.1     ; time constant, in ps
ref_t           = 318   318     ; reference temperature, one for each
group, in K
nsttcouple      = 0.9999        ; 1 by default
; Pressure coupling is off
pcoupl          = berendsen     ; Berendsen thermostat
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
; Periodic boundary conditions
pbc             = xyz           ; 3-D PBC
; Dispersion correction
DispCorr        = EnerPres      ; account for cut-off vdW scheme
; Velocity generation
gen_vel         = no            ; assign velocities from Maxwell distribution
gen_temp        = 300           ; temperature for Maxwell distribution
gen_seed        = -1            ; generate a random seed

Could you please guide me to solve the problem?


-- 
Ankita Naithani