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:
- 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.
- 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.