Hwo to Pull Peptide from the Middle?

User discussions
1

GROMACS version: 2022.6
GROMACS modification: ?

Hi everyone,

Successfully performed pulling molecular dynamics (MD) on a peptide docked to a protein. Now seeking guidance on adjusting .mdp file for pulling the peptide from the middle. Any suggestions?

2

If it’s just pulling from the middle without biasing the orientation, the pull code with two groups with both COMs and a coordinate for the distance will do it. You can do steered MD by setting the pull rate or do adaptive sampling with AWH. There are tutorials for AWH.