<br><br>Hi <br><br>I am setting <font style="background-color: rgb(255, 255, 51);" size="4">pbc = xyz</font> ; and type the commands<br><br>grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 6LYZ-EM-solvated <br>
<br>mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated <br><br>=> the simulation failed and .out file suggested me to use the flag -pd.<br><br><br><br><br>grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 6LYZ-EM-solvated <br>
mpiexec -np 16 mdrun_mpi <font style="background-color: rgb(255, 255, 51);" size="4">-pd</font> -v -deffnm 6LYZ-EM-solvated <br>
<br>=> the simulation runs well.<br><br><br>Why?<br><br><br>Thank you<br>Lin<br><br><br><br><br>