[gmx-users] There is no domain decomposition for nodes that is compatible

[Steven Neumann]

Can you please advise? With large constraints it does not work... with [
distance_restraints ] it works but only with mdrun -nt 1
my mdp:

disre                =  simple
disre-fc             =  1000

integrator               = md
tinit                    = 0.0
dt                       = 0.008
nsteps                   = 100000      ; 500 ns
nstcomm                  = 100
nstcalcenergy         = 100

nstxout             = 0
nstvout               = 0
nstenergy            = 0
nstlog                   = 100
nstxtcout                = 100

freezegrps         = System
freezedim          = N N Y
energygrps               = ACI BAS GLY NON POL
energygrp_table          = ACI ACI ACI BAS ACI GLY ACI NON ACI POL BAS BAS
BAS GLY GLY GLY GLY NON GLY POL NON BAS NON NON POL BAS POL NON POL POL
table-extension         = 1.0


nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 2.0


coulombtype          = User
rcoulomb                 = 2.0

vdw_type                 = User
rvdw                     = 2.0


tcoupl               = V-rescale
tc_grps               = System
tau_t                 = 0.1
ref_t                 = 300
pcoupl             = no

gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = -1


constraints              = none
constraint_algorithm     = Lincs
continuation             = no
lincs_iter              = 1
lincs_order              = 4





I will really appreciate.

Steven


On Wed, Feb 5, 2014 at 12:55 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> Dear Users,
>
> I am simulating a nanotube with bonds and LINCS = all-bonds. Because the
> tube is bending I tried to apply bonds or LINCS constraints between atoms
> lying oppositely within the circles (tube diameter) so I used just one to
> check:
>
> [ bonds ]
> 2485    2451    1    7.46    50000
>
> And I get:
>
> There is no domain decomposition for 8 nodes that is compatible with the
> given box and a minimum cell size of 10.2576 nm
> Change the number of nodes or mdrun option -rdd or -dds
> Look in the log file for details on the domain decomposition
>
>
> Why LINC does not work for longer bonds - across diameter? Please, advise?
> Would you suggest distance restraints instead?
>
> Thanks,
>
> Steven
>