GROMACS version: 2025.3
GROMACS modification: No
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = Chain_B(Memb)
pull_group2_name = Chain_A(Lig)
pull-pbc-ref-prev-step-com = yes
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = cylinder ; simple distance increase
pull_coord1_dim = N N Y ; pull along z
pull_coord1_groups = 1 2 ; groups 1 (Chain A) and 2 (Chain B) define the reaction coordinate
pull-coord1-vec = 0.0 0.0 1.0
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = -0.0005 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 500 ; kJ mol^-1 nm^-2
These are my pulling simulation, i tried using negative sign in the pulling vectors but had no luck. I tried different combinations like direction , direction-periodic , cylinder. I interchanged the pull groups but eveerytime the ligand moves upwards i.e away from the membrane and then exits the box and enters the box from the opposite side. I tried reducing the rate and the force but no luck. When i had placed the ligand just above the membrane surface, I had no issues in getting the ligand pass and atleast reach the middle portion. But now since I intent to pull ligand from the water phase and then bring it toward the membrane , i fail in doing so. Any kind of advice at this point of time will be very helpfull. Thanks in advance!!!