PBC along xy direction and create walls at z=60 and z=-60

User discussions
1

GROMACS version:2020.1-Ubuntu-2020.1-1
GROMACS modification: Yes/No
I want to apply PBC along XY direction and need to create sulfur walls at z=60 and z=-60. To apply PBC in xy directions we have to set pbc=xy in mdp option file. Along with this, if we set nwalls=2 then it creates walls at z=0 and z=z-box but I need to create walls at z=60 and z=-60. Please suggest how to set walls at the desired position?

2

Hello,

set box-z to 120 and use z=60 as your reference point for any analysis and creating the rest of your system. There might be a way to use e.g. a tabulated potential to create the wall at -60 but I believe it would be far easier and importantly safer to work with the standard Gromacs workflow.

Regards,
Petter