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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