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

[Justin A. Lemkul]

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)
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================