# Mdp parmaters in steered MD **URL:** \ **Category:** User discussions\ **Created:** [February 1, 2023, 10:57am UTC](https://gromacs.bioexcel.eu/t/mdp-parmaters-in-steered-md/5696 "2023-02-01T10:57:40Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![himanshi09](https://avatars.discourse-cdn.com/v4/letter/h/7c8e57/32.png) [@himanshi09](https://gromacs.bioexcel.eu/u/himanshi09)\ **Post date:** [February 1, 2023, 10:57am UTC](https://gromacs.bioexcel.eu/t/mdp-parmaters-in-steered-md/5696/1 "2023-02-01T10:57:40Z")
GROMACS version: 2018 GROMACS modification: Yes/No Hello, I am working with membrane protein-ligand complex in gromacs using Dr J Lemkul tutorials. I want to perform umbrella sampling on the same to pull the ligand from binding site of the protein. The issues which I am facing: 1. During the equilibration step, I made an index file containing lipid, protein and ligand. And the same index file I am using for pulling the simulation. So I am not sure if I have defined the groups correctly in my md\_pull.mdp file. 2. one of the loops of my protein is breaking after applying the pulling code. Pull code: Tcoupl = Nose-Hoover tc\_grps = Protein\_AKU6\_DPPC Water\_and\_ions tau\_t = 1.0 1.0 ref\_t = 300 300 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau\_p = 2.0 compressibility = 4.5e-5 ref\_p = 1.0 Pull code pull = yes pull\_ncoords = 1 ; only one reaction coordinate pull\_ngroups = 2 ; two groups defining one reaction coordinate pull\_group1\_name = AKU6 pull\_group2\_name = Protein pull\_coord1\_type = umbrella ; harmonic potential pull\_coord1\_geometry = distance ; simple distance increase pull\_coord1\_dim = N N Y pull\_coord1\_groups = 1 2 pull\_coord1\_start = yes ; define initial COM distance \> 0 pull\_coord1\_rate = 0.005 ; 0.005 nm per ps pull\_coord1\_k = 600 ; kJ mol^-1 nm^-2 Any help would be appreciated. Thank you.