[gmx-users] Domain Decomposition does not support simple neighbor searching.

[Daniele Veclani]

Dear Gromacs Users

I'm trying to do a simulation in a  NVE ensemble in vaccum. But I but
I find this
error:

"Domain Decomposition does not support simple neighbor searching, use grid
searching or run with one MPI rank"

If I use ns_type=grid I can generate the .tpr file, But when I run mdrun I
find:

"NOTE: This file uses the deprecated 'group' cutoff scheme. This will be
removed in a future release when 'verlet' supports all interaction forms.

and mdrun program crashes.


How can I do  energy minimization  and  simulation in NVE ensemble in
vaccum with GROMACS 5.0.4?

This is my .mdp file for energy minimization:

; Run control
integrator               = steep
nsteps                   = 500000
; EM criteria and other stuff
emtol                    = 10
emstep                   = 0.001
niter                    = 20
nbfgscorr                = 10
; Output control
nstlog                   = 1
nstenergy                = 1
; Neighborsearching PARAMETERS
cutoff-scheme            = group
vdw-type                 = Cut-off
nstlist                  = 1        ; 10 fs
ns_type                  = grid     ; search neighboring grid cells
pbc                      = No
rlist                    = 0.0       ; short-range neighborlist cutoff (in
nm)
rlistlong                = 0.0
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype              = cut-off ; Particle Mesh Ewald for long-range
electrostatics
rcoulomb-switch          = 0
rcoulomb                 = 0.0        ; short-range electrostatic cutoff
(in nm)
rvdw                     = 0.0        ; short-range van der Waals cutoff
(in nm)
rvdw-switch              = 0.0
epsilon_r                = 1
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                  = No
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12
; EWALD/PME/PPPM parameters
pme_order                = 6
ewald_rtol               = 1e-06
epsilon_surface          = 0
; Temperature and pressure coupling are off during EM
tcoupl                   = no
pcoupl                   = no
; No velocities during EM
gen_vel                  = no
 Bond parameters
continuation             = no            ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints
constraints              = h-bonds     ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter               = 2             ; accuracy of LINCS
lincs_order              = 4             ; also related to accuracy


To use a single MPI is correct to do so:

-mpirun -np 1 mdrun -s *.trp ??

There still exists the possibility of using the Point Decomposition method
(mdrun -pd) in gromacs 5.x?

Best regards
D.V.