GROMACS version:2022.2
GROMACS modification: No
I was trying to simulate Silicon Nitride (Si3N4) in gromacs in order to calculate its dielectric constant. I created a triclinic slab from the inorganic builder plugin in vmd, and defined a triclinic box by using -box and -angle (90 90 60) using gmx editconf. I created topology using pdb2gmx since I defined the unit cell and bonds in aminoacids.rtp as I was using gromacs port of Charmm36m. I defined bonded and non-bonded interactions following this tutorial:[https://www.ks.uiuc.edu/Training/Tutorials/nanobio/bionano-tutorial.pdf], converted the units as per gromacs. After minimization, my structure was getting out of its original shape and the simulation box. So, to determine if this is a parameter issue or not, I chose to freeze the atoms. I don’t expect a minimization step, since every atom is frozen,which is the case, but I do see that the atoms are not in the box after the process. Can anyone help me to understand what is the issue here? The box dimensions defined in the last line of the gro file r
emains same, as evident in the image attached. I am attaching relevant files.[files - Google Drive]