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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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