i generated a lammps system using charmmgui for a ~10000 atoms protein with 40 angstroms of water around it so that my protein has plenty of space to swim around. im trying to use fix wall/harmonic at the edges of the simulation box to avoid parts of the protein wrapping around periodic boundary conditions. one problem with the input generated by charmmgui is that some water molec…

Dear all I study supercapacitors using MD simulation and lammps. I want to calculate electric potential profile along z axis. How can I do this? Thank you in advance for your help. Malidadi 1 post - 1 participant Read full topic