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

[Chih-Ying Lin]

Hi
I was currently updatiing the 3.3.3 version to 4.0.5 version.
My system is "one protein + TIP3P water".
The protein structure is from 6LYZ.pdb



The ,gro file and .top file are created from pdb2gmx.
Then, I do the following steps,
Energy minimization of the structure (vacuum)
Periodic boundary conditions
Solvent addition
Addition of ions: counter charge
Energy minimization of the solvated system
Relaxation of solvent and hydrogen atom positions: Position restrained MD



This "one protein + TIP3P water" system is running no problems  with 3.3.3.
But, the  Fetal Error "A charge group moved too far between two" comes
from 4.0.5.


All the commands are from the tutorials =>
http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/


Although my system is blowing, which is suggested by
oldwiki.gromacs.org, i think the protein structure is OK, I have no
ideas about which steps I was doing wrong.

Any ideas about this?


Thank you
Lin







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
> -------------------------------------------------------
>
>

Well, you're being given a pretty explicit hint.  This is a very useful error
message.  You're system is blowing up.  I'd point to the relevant wiki site, but
it appears that oldwiki.gromacs.org is not operating...

In any case, better minimization and/or equilibration is necessary, as mdrun has
told you.

-Justin

>
>
>
> ; 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)
>