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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