[gmx-users] load imbalance

[E. Nihal Korkmaz]

Hi all,

I am trying to run GB model simulation of a small protein. I keep getting
these errors for every step printed to the log file.

DD  load balancing is limited by minimum cell size in dimension X
DD  step 35999  vol min/aver 0.799! load imb.: force 154.9%

Below i copied my mdp parameters. I'd appreciate any suggestion to help me
fix this.

Thanks,
Nihal


integrator               = sd
tinit                    = 0
dt                       = 0.002
nsteps                   = 5000000
simulation_part          = 1
init_step                = 1 %start from 5ns


nstxout                  = 5000
nstvout                  = 5000
nstenergy                = 500
nstxtcout                = 500
nstlog                   = 500

xtc_grps                 = System
energygrps               = System
comm_mode                = Linear
; neighbor searching and vdw/pme setting up
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 2.0

coulombtype              = pme
fourierspacing           = 0.1
pme_order                = 6
rcoulomb                 = 2.0

vdwtype                  = Cut-off
rvdw_switch              = 1.0
rvdw                     = 2.0

; cpt control
tcoupl                   = Berendsen
tc-grps                  = System
tau_t                    = 0.1
ref_t                    = 300.0
Pcoupl                   = Berendsen
pcoupltype               = isotropic
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0

; velocity & temperature control
gen_vel                  = yes
gen_temp                 = 300.0
annealing                = no
constraints              = hbonds
constraint_algorithm     = lincs
morse                    = no


-- 
Elif Nihal Korkmaz

Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone:  608-265-3644
Email:   korkmaz at wisc.edu
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