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
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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.
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I have searched gmx online but could not find any clue! Can anybody help me?
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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