Dear all, I want to ask a question about the write_data command. Imagine, there is a box with p p p boundary condition. One molecular with four atoms (bonds 1-2-3-4, bond length A) is near the top of the box. After some time steps, atom 1 leaves the top of the box. Because of the periodic boundary conditions, a new atom 1 will appear at the bottom of the box. And the distance bet…

Hi Victor, I’m replying to the list, since your questions are general and answers are most useful to everyone. Dear Dr. Giacomo, Hi Dr. Giacomo. Victor here and sorry to disturb you again. I have some questions on the PMF output value from the file out.h_pot.ti.pmf from LAMMPS Colvars module Umbrella Sampling method: So my case is to drag the polymer molecule (polyacrylamide+a…

Dear colleagues, I have questions about the LAMMPS -partition flag and “how to multiple”. I am using version 7Aug19. Suppose I have 10 complete scripts (run1in.npt … run10in.npt) in a given directory. I would like to run 2 simulations at a time in this universe of scripts, and after each one is finished, continue running the others. To run 2 simulations at a time I use the “-pa…