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

[Mark Abraham]

Chih-Ying Lin wrote:
> 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
> -------------------------------------------------------

I haven't seen much of this error, but it seems akin to the usual 
"blowing up" symptoms one gets when a starting structure is 
poorly-conditioned with respect to its physics. This generates large 
forces and velocities, and something breaks. Here, some charge group has 
moved too far.

You need to look carefully at your structures and see what, if anything, 
looks wrong. If this error occurred after few integration steps (see the 
.log file) then your starting structure has a problem. Try a vacuum 
simulation, or solvating differently. Without knowing how you've 
prepared the system, it's impossible to give concrete advice.

Mark


> ; 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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