[gmx-users] Topology question

[Xiaoyun Yuan]

Hi,

I have generated a crystal solid surface and had it sit on xy planner of the box in gromacs. After that I randomly inserted some optimized molecules. Now when I try to minimize the energy of the system, a fatal error showed up: the number of coordinates in .gro file does not match topology, and topology has more atoms involved. The surface input file does not have any connectivities, so I cannot generate .itp file for it, which means I cannot edit the .top file and add molecules to the system even though I have inserted both surface and molecules to the box. I am not interested in the surface energy, is it possible to fix this error without .itp file for the surface? Can I freeze it?

Thanks in advance.

Sincerely,
Kelsy