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? Thank you Lin
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