[gmx-users] Problem with mdrun!

[David van der Spoel]

Blaise Mathias-Costa wrote:
> Hello All,
> The program was stopped twice with the following error:
> 
>    
> Constraint error in algorithm Lincs at step 54646
> 
> t = 109.292 ps: Water molecule starting at atom 13293 can not be settled.
> Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
> previous and current coordinates
> Grid: -2147483648 x -2147483648 x -2147483648 cells
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 3.3.1
> Source code file: nsgrid.c, line: 220
> 
> Fatal error:
> Number of grid cells is zero. Probably the system and box collapsed.
> 
> -----
> I have searched gmx online but could not find any clue! Can anybody help me?

try the wiki as well. you probably need more equilibration with posres 
and reduce the emtol if you do EM.
> 
> The system has two protein molecule, a drug, ligand glycine, and water. 
> I have done
> sd, cg, pr, & sa before md! One thing that i could note that the cg 
> stopped in 385 steps though the emtol was set 500, but nsteps 10000 !
> 
> The unit cell has: ~ 106000 atoms and here is the .mdp file
> 
> 
> cpp                      = cpp
> include                  = -I../top
> define                   =
> integrator               = md
> dt                       = 0.002
> nsteps                   = 50000000
> nstxout                  = 5000
> nstvout                  = 5000
> nstlog                   = 5000
> nstenergy                = 500
> nstxtcout                = 250
> xtc_grps                 = Protein
> energygrps               = Protein  SOL DRG Cl
> nstlist                  = 10
> ns_type                  = grid
> rlist                    = 0.8
> coulombtype              = cut-off
> rcoulomb                 = 1.4
> rvdw                     = 0.8
> tcoupl                   = Berendsen
> tc-grps                  = Protein SOL DRG Cl
> tau_t                    = 0.1 0.1 0.1 0.1
> ref_t                    = 300 300 300 0.1
> Pcoupl                   = Berendsen
> tau_p                    = 1.0
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> gen_vel                  = yes
> gen_temp                 = 300
> gen_seed                 = 173529
> constraints              = all-bonds
> --------------------------
> 
> Many thanks in advance!
> 
> 
> Kind Regards,
> Blaise
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se