[gmx-users] nvt error

[Urszula Uciechowska]

Hi,

During nvt simulations I obtained an error message:

-------------------------------------------------------
Program mdrun_mpi, VERSION 5.0.6
Source code file:
/scratch/60488192.batch.grid.cyf-kr.edu.pl/gromacs-5.0.6/src/gromacs/mdlib/pme.c,
line: 754

Fatal error:
11 particles communicated to PME rank 3 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge
 group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Error on rank 15, will try to stop all ranks
Halting parallel program mdrun_mpi on CPU 15 out of 32


-------------------------------------------------------
Program mdrun_mpi, VERSION 5.0.6
Source code file:
/scratch/60488192.batch.grid.cyf-kr.edu.pl/gromacs-5.0.6/src/gromacs/mdlib/pme.c,
line: 754

Fatal error:
1 particles communicated to PME rank 4 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge
group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Error on rank 19, will try to stop all ranks
Halting parallel program mdrun_mpi on CPU 19 out of 32



My nvt input file is:

; 7.3.2 Preprocessing
define                  = -DPOSRES

; 7.3.3 Run Control
integrator              = md
tinit                   = 0
dt                      = 0.002
nsteps                  = 100000
comm_mode               = Linear
nstcalcenergy           = 1
comm_grps               = Protein Non-Protein

; 7.3.8 Output Control
nstxout                 = 25000
nstvout                 = 25000
nstfout                 = 25000
nstlog                  = 100
nstenergy               = 100
nstxtcout               = 100
xtc_precision           = 1000
xtc_grps                = System
energygrps              = System
cutoff-scheme           = verlet
; 7.3.9 Neighbor Searching
nstlist                 = 10
ns_type                 = grid
pbc                     = xyz
rlist                   = 0.9

; 7.3.10 Electrostatics
coulombtype             = PME
rcoulomb                = 0.9

; 7.3.11 VdW
vdwtype                 = cut-off
rvdw                    = 0.9
DispCorr                = EnerPres

; 7.3.13 Ewald
fourierspacing          = 0.12
pme_order               = 4
ewald_rtol              = 1e-5

; 7.3.14 Temperature Coupling
tcoupl                  = V-rescale
tc_grps                 = Protein    Non-Protein
tau_t                   = 0.1        0.1
ref_t                   = 300        300

; 7.3.17 Velocity Generation
gen_vel                 = yes
gen_temp                = 310
gen_seed                = -1

; 7.3.18 Bonds
constraints             = all-bonds
constraint_algorithm    = LINCS
continuation            = no
lincs_order             = 4
lincs_iter              = 1
lincs_warnangle         = 30

What is wrong in the input file?


Thank you for any suggestions.

best
Urszula



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