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

[Mark Abraham]

Chih-Ying Lin wrote:
> 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
> -------------------------------------------------------

This looks pretty explicit to me. You've chosen ns_type = simple below, 
and that only works for particle decomposition. So either use PD, or 
ns_type = grid. What's the problem?

Mark

> 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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