GROMACS version:
GROMACS modification: Yes/No
I have constructed a mixed system that contains SiO2, polymer, and water using the “gmx insert-molecule” and “gmx solvate” functions of Gromacs. However, I encountered a problem after performing the NPT ensemble simulation to equilibrate the system. The system exhibits a vacuum area, which I believe is due to the box density being lower than 1g/mL. Additionally, the presence of the SiO2 structure hinders the box from shrinking to a reasonable size. How can I get a well-defined box with reasonable density? which the simulation box has an adjustable size along with Z axis. Thanks for your helps
