[gmx-users] pbc = xyz with mdrun -pd ?

[Chih-Ying Lin]

Hi

I am setting pbc = xyz ; and type the commands

 grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o
6LYZ-EM-solvated
  mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated
 => the simulation failed and .out file suggested me to use the flag -pd.


grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o
6LYZ-EM-solvated
  mpiexec -np 16 mdrun_mpi -pd -v -deffnm 6LYZ-EM-solvated
  =>  the simulation runs well.


  Why?


I am doing Energy minimization of the solvated system ( a protein molecule +
TIP3P water) and the .mdp file and  error is as follows.


Thank you
Lin

-------------------------------------------------------
Program mdrun_mpi, VERSION 4.0.5
Source code file: domdec.c, line: 5459

Fatal error:
ns type Simple is not supported with domain decomposition,
use particle decomposition: mdrun -pd
-------------------------------------------------------




cpp             = /lib/cpp      ; Preprocessor

; Definea can be used to control processes
define          = -DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator      = steep         ; Algorithm (steep = steepest descent
minimization)
emtol           = 1.0           ; Stop minimization when the maximum force <
1.0 kJ/mol
nsteps          = 500           ; Maximum number of (minimization) steps to
perform
nstenergy       = 1             ; Write energies to disk every nstenergy
steps
energygrps      = System        ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the
interactions
nstlist         = 5             ; Frequency to update the neighbor list and
long range f
orces
ns_type         = simple        ; Method to determine neighbor list (simple,
grid)
rlist           = 1.0           ; Cut-off for making neighbor list (short
range forces)
coulombtype     = cut-off       ; Treatment of long range electrostatic
interactions
rcoulomb        = 1.0           ; long range electrostatic cut-off
rvdw            = 1.0           ; long range Van der Waals cut-off
constraints     = none          ; Bond types to replace by constraints
pbc             = xyz           ; Periodic Boundary Conditions (yes/no)
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