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

[Justin Lemkul]

On 8/21/12 12:59 PM, virginia miguel wrote:
> 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.
>

Your timestep (5 fs) is too large.  Reduce it to 2 fs and try again.

-Justin

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

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