[gmx-users] Domain decomposition fatal error during production run

[Nawel Mele]

Dear gromacs users,

I performed a MD simulation on a dimer system with pulling code during the
production run to force the two monomers to get closer. After 55 ns of
production run I got this error :



















*step 30616369: Water molecule starting at atom 30591 can not be
settled.Check for bad contacts and/or reduce the timestep if
appropriate.Wrote pdb files with previous and current coordinatesStep
30616370:The charge group starting at atom 669 moved more than the distance
allowed by the domain decomposition (1.000000) in direction Zdistance out
of cell 10.671883Old coordinates:    4.987    7.414    5.096New
coordinates:   10.939    9.096   19.806Old cell boundaries in direction
Z:    3.808    9.132New cell boundaries in direction Z:    3.822
9.134-------------------------------------------------------Program mdrun,
VERSION 4.6.5Source code file:
/gem/00_installers/gromacs/gmx-centos6/gromacs-4.6.5/src/mdlib/domdec.c,
line: 4412Fatal error:A charge group moved too far between two domain
decomposition stepsThis usually means that your system is not well
equilibrated*

Here is my mdp input file:

title               =  Protein in water - Production Run
cpp                 =  cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  50000000 ; total 100 ns.
nstcomm             =  1
nstxout             =  500000     ; 1 ns
nstvout             =  2500     ; 5 ps
nstfout             =  0
nstlog              =  2500     ; 5 ps
nstenergy           =  2500     ; 5 ps
nstxtcout           =  2500     ; 5 ps
xtc-precision       =  1000
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
coulombtype         =  PME
rcoulomb            =  1.0
rvdw                =  1.0
; Temperature coupling
Tcoupl              =  nose-hoover
tc-grps             =  system
tau_t               =  0.1
ref_t               =  300
; Energy monitoring
energygrps          =  Protein  Non-Protein
; Isotropic pressure coupling
Pcoupl              =  Parrinello-Rahman
Pcoupltype          =  isotropic
tau_p               =  1.0
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 300 K.
gen_vel             =  no

gen_temp            =  300.0
gen_seed            =  173529
; Mode for center of mass motion removal
comm-mode            =  Linear
; Pull code
pull                    = umbrella
pull_geometry           = distance  ; simple distance increase
pull_dim                = N N Y     ; pull along z
pull_group0             = Chain_B
pull_group1             = Chain_A
pull_vec1               = 0.0 0.0 -1.0
pull_ngroups            = 1         ; two groups defining one reaction
coordinate
pull_start              = yes       ; define initial COM distance > 0
pull_rate1              = -0.01      ; 0.01 nm per ps = 10 nm per ns due to
the minus sign it pulls to opposite direction
pull_k1                 = 1000      ; kJ mol^-1 nm^-2


I am confused with what exactly happen here, when I looked at the COM
distance between the two monomers it is fluctuating around 2.6 nm but does
not go higher than 3 nm or less than 2.5 nm. Can anyone help me here?

Many thanks,

Regards,

Nawel
-- 

Dr Nawel Mele,
T: +33 (0) 634443794 (Fr)

+44 (0) 7704331840 (UK)