I’m new to LAMMPS. For one of my project, I am working on MD simulation to find out the mechanical properties of Magnesite. Firstly, I generated a pdb file of Magnesite using Avogadro and increased atom numbers using packmol. After that, I converted this pdb file to LAMMPS readable data file using VMD. Since, VMD doesn’t provide bond and angle information, that’s why I manually put all of those information in the input script. I used buckingham potential for that mineral with some parameters from other papers. But, when I run this simulation, each time I am getting these two errors/warnings. I went through all of the previous mailist of this forum, but, still couldn’t find the actual problem in this simulation. Would you like to help me to fix this problems? I have attached the input script and data file for your convenience.
data(full).data (11.0 KB)
Magnesite.txt (1.1 KB)
The problem is in your data file. It defines a box of 1x1x1 angstrom. That is obviously not correct.
You probably loaded a file into VMD that does not contain box information and didn’t set it as needed.
However, there are other obvious issues:
- why change the box to triclinic?
- you are using long-range electrostatics and a kspace style, but none of your atoms have (partial) charges applied. And for your kind of system, there should be
- you would get neighborlist overflows due to the small box. I assume that is why you increase the neighbor list page
- you have created bonds/angles/dihedrals for individual units and bonds that look very unrealistic for the system at hand. where did you get those parameters for Mg-O bonds, for example?
Thank you for your response. I may solve some of your mentioned issues that you find . Just, would you like to inform me how can I set charge for all of the atom types? Is it possible to get charges of the atoms from VMD or I have to set it in lammps input script using set/charge command? Thank you.
Please see the documentation of the read_data command — LAMMPS documentation
I also strongly advise you to find a suitable tutor with experience in MD simulations. As this example shows, just modifying the input until errors go away does not result in a meaningful simulations. There are many more possibilities for errors, especially with details of the force field and details pertaining to statistical mechanics and statistical thermodynamics, that won’t show as easily as when LAMMPS crashes or prints warnings. Without you are likely make (many) errors unnoticed and thus are very likely to waste a lot of time or - even worse and very embarrassing - may try to publish incorrect conclusions.