I have been performing Umbrella Sampling simulations of a host-guest system. Regarding the stage of the steered molecular dynamics simulation, I would like to know how to pull a group along the z coordinate in the opposite direction (x , y , -z).
This is my current pull.mdp file:
; Pull code
pull = yes ; Tells grompp to read settings for COM pulling
pull_ncoords = 1 ; Only one reaction coordinate
pull_ngroups = 2 ; Two groups defining one reaction coordinate
pull_group1_name = CNH ; Name of the first group used by the pull code.
pull_group2_name = CI3 ; Name of the second group used by the pull code.
pull_coord1_type = umbrella ; Use harmonic potential to pull
pull_coord1_geometry = distance ; Simple distance increase
pull_coord1_dim = N N Y ; Applying a bias only in the z-dimension
pull_coord1_groups = 1 2 ; The reaction coordinate connects groups 1 and 2.
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
Maybe I could do that, but that would involve to rebuild all of my system. Since the force is applied in a unwanted direction, I thought it would be possible to define an opposite direction in the input file for the steered MD simulation. Here is a snapshot of my system:
Thank you for your response. Actually, I did not find a solution for this question during this time. Thus, I started to conduct these simulations using the Amber software, which I have more experience. Fortunately, I don’t have this problem anymore in this software.
hi since gromacs takes Y and N to define x y z pulling. please guide. I am flipping my system 180 degrees. but is there a way to define negative coordinates?
