[gmx-users] Trouble with domain decomposition in direction X

[virginia miguel]

Hi everyone; I am running a MD simulation of a 40 kDa protein bound to ADP  in GROMACS VERSION 4.5.5. I made three minimization  with restrains in protein, backbone and c-alpha, in that order, and two equilibration with 150 and 300K using backbone restrains. But when I run my md I get this error

(...)

Step 234604:
The charge group starting at atom 3430 moved than the distance allowed by the domain decomposition (3.219980) in direction X
distance out of cell -65.799425
Old coordinates:    4.304    3.918    3.886
New coordinates:  -62.579    4.743    6.132
Old cell boundaries in direction X:    3.220    6.439
New cell boundaries in direction X:    3.220   
 6.440

-------------------------------------------------------
Program mdrun, VERSION 4.5.5
Source code file: domdec.c, line: 4124

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


The atom corresponds to the ADP

the mdp file I am using is the following and I am running it with

mdrun -nt 4 -npme 1 -v -s topol.tpr -o traj.trr -x traj.xtc -c din.pdb -e ener.edr -g md.log



;
;    User spoel (236)
;    Wed Nov  3 17:12:44 1993
;    Input file
;
title               =  Yo
define              = 
 
integrator          =  md
dt                  =  0.005    
nsteps              =  40000000
nstxout             =  20000
nstvout             =  20000
nstfout             =  0
nstxtcout           =  500
nstlog              =  1000
nstenergy           =  500
nstlist            
 =  4
ns_type             =  grid
energygrps          =  Protein  SOL 
coulombtype         =  pme
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  1.4
; Berendsen temperature coupling is on in two groups
Tcoupl              =  V-rescale
tc-grps            =  !SOL    SOL
tau_t               =  0.1   
 0.1
ref_t               =  300    300
; Energy monitoring
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          =  isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed           
 =  173529

constraints         =  all-bonds



If any one can help me with this error I would appreciate it very much!. Thank you in advance, Virginia.

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