Finite Flat-Bottomed Position Restraint

User discussions
1

GROMACS version: 2023
GROMACS modification: No

Hey guys,

I’m new in Gromacs and I wanted to know if the Heaviside step function from the flat-bottomed position restraint can be modified. We need to simulate the translocation of a knotted protein but from the outside of the geometry towards its inside, so infinite structures doesn’t apply because the protein would be inside the whole time. If anyone could help >.<

Best regards,

Cayetana

2

There is too little information in your post to understand what you want to do. Translocation through what?
If I guess correctly what you want to do, the COM pull code would be the suitable tool.