GROMACS version: 2020.1
GROMACS modification: Yes/No
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I am trying to calculate position-dependent diffusivity and PMF on a system of probe molecule and slab. As I am expecting harmonic potential should be applied to the probe molecule for keeping desired distance, but not on the slab, I am not sure which group pull code chooses to apply harmonic potential. I am keeping the center layer of slab position restraint.
pull = yes pull_ncoords = 1 pull_ngroups = 2 pull-nstxout = 1 pull_group1_name = SLAB pull_group2_name = PROBE pull_coord1_groups = 1 2 pull_coord1_type = umbrella pull_coord1_geometry = distance pull_coord1_dim = N N Y pull_coord1_start = yes pull_coord1_rate = 0.0 pull_coord1_k = 2000
I am wondering if the choice of pull_coord1_groups = 1 2 or 2 1 has any effects on how pull-code chooses to apply harmonic potential.