[gmx-users] Energy minimization with Walls

John Adams john.adams1395 at gmail.com
Fri Mar 23 17:11:20 CET 2018

I am trying to put together a mdp script for energy minimization using 2
walls in the z direction. I have a slab of just water which is simulated
fine if i remove the walls section from the script. when I add the wall
section, I start to receive this error

"Fatal error:
DD cell 4 4 0 could only obtain 19 of the 20 atoms that are connected via
vsites from the neighboring cells. This probably means your vsite lengths
are too long compared to the domain decomposition cell size. Decrease the
number of domain decomposition grid cells.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors"

My script

;title          = Minimization  ; Title of run

define = -DFLEXIBLE
; Parameters describing what to do, when to stop and what to save
integrator      = steep         ; Algorithm (steep = steepest descent
emtol           = 100.0         ; Stop minimization when the maximum force
< 1.0 kJ/mol
emstep          = 0.01      ; Energy step size
nsteps          = 50000         ; Maximum number of (minimization) steps to
energygrps      = system        ; Which energy group(s) to write to disk

nstlist         = 1
ns_type         = grid
rlist           = 1.0
coulombtype     = PME
rcoulomb        = 1.0
rvdw            = 1.0

pbc             = xy            ; pbc in xy only
nwall           = 2             ; wall at z=0 and z=z-box
wall-type       = 10-4          ; direct 12-6 LJ as fn of distance from wall
wall-density    = 20 20
wall-atomtype   = CA CA
wall-r-linpot   = 1
ewald-geometry  = 3dc           ; Only Ewald sum compatible with slab
geometry, requires box_height >= slab_height * 3
wall-ewald-zfac = 3             ; Extra empty space for slab geometry
calculation (reducing coulomb interaction)

I hope someone could help me figure what is the problem


More information about the gromacs.org_gmx-users mailing list