[gmx-users] A charge group moved too far between two domain decomposition steps

[Chih-Ying Lin]

Hi
In the system, one lysozyme + TIP3P water.

After the two commands,
grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr
mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR




pr.mdp, minim.mdp  and the error information is as follows.
nsteps          = 5000          ; Maximum number of (minimization) steps
How to solve the problem?

Thank you
Lin



-------------------------------------------------------
Program mdrun_mpi, VERSION 4.0.5
Source code file: domdec.c, line: 3651

Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
-------------------------------------------------------





; VARIOUS PREPROCESSING OPTIONS
title                    =
cpp                      = /lib/cpp
include                  =
define                   = -DPOSRES

; RUN CONTROL PARAMETERS
integrator               = md
tinit                    = 0
dt                       = 0.001
nsteps                   = 5000
nstcomm                  = 0

; OUTPUT CONTROL OPTIONS
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
nstlog                   = 10
nstenergy                = 1
nstxtcout                = 0
xtc_precision            = 1000
xtc-grps                 = System
energygrps               = Protein Non-Protein

; NEIGHBORSEARCHING PARAMETERS
nstlist                  = 5
ns-type                  = Grid
pbc                      = xyz
rlist                    = 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype              = Reaction-Field
rcoulomb                 = 1.4
epsilon_rf               = 78
epsilon_r                = 1
vdw-type                 = Cut-off
rvdw                     = 1.4

; Temperature coupling
Tcoupl                   = Berendsen
tc-grps                  = Protein  Non-Protein
tau_t                    = 0.1      0.1
ref_t                    = 200      200

; Pressure coupling
Pcoupl                   = No

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = yes
gen_temp                 = 200.0
gen_seed                 = 1735

; OPTIONS FOR BONDS
constraints              = all-bonds
constraint-algorithm     = Lincs
unconstrained-start      = no
lincs-order              = 4
lincs-iter               = 1
lincs-warnangle          = 30






; LINES STARTING WITH ';' ARE COMMENTS
title           = Minimization of Lysozyme (1LW9.pdb)   ; Title of run

; The following lines tell the program the standard locations where to find
cert
ain files
cpp             = /lib/cpp      ; Preprocessor

; Definea can be used to control processes
define          = -DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator      = steep         ; Algorithm (steep = steepest descent
minimizati
on)
emtol           = 1.0           ; Stop minimization when the maximum force <
1.0
 kJ/mol
nsteps          = 5000          ; Maximum number of (minimization) steps to
perf
orm
nstenergy       = 1             ; Write energies to disk every nstenergy
steps
energygrps      = System        ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calcul
ate the
interactions
nstlist         = 5             ; Frequency to update the neighbor list and
long
 range forces
ns_type         = simple        ; Method to determine neighbor list (simple,
gri
d)
rlist           = 1.0           ; Cut-off for making neighbor list (short
range
forces)
coulombtype     = cut-off       ; Treatment of long range electrostatic
interact
ions
rcoulomb        = 1.0           ; long range electrostatic cut-off
rvdw            = 1.0           ; long range Van der Waals cut-off
constraints     = none          ; Bond types to replace by constraints
pbc             = xyz           ; Periodic Boundary Conditions (yes/no)
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