Pull Code for Umbrella Sampling: Choosing atom as group

User discussions
1

GROMACS version: 2018.4
GROMACS modification: No

I am using the umbrella sampling tutorial and I have a question:
I’m wondering if there is a way to specify an atom in a group rather than a whole group in the pull-code? For example, I am interested in a ligand binding to a surface atom of a metal-oxide slab (instead of looking at its distance to the center of mass of the slab)

How would I modify this:
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = Chain_A
pull_group2_name = Chain_B
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; 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_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

2

You can use gmx make_ndx to define your own groups in an index file. You can define a group containing only 1 atom, and as long as the index file is included in the commands, you will be able to use it in the mdp file.

3

pull_coord1_k = 1000，what does it mean？Could I see it as elastic constant，THanks

4

Yes, in the case where pull_coord1_type is set to umbrella, this is the force constant to the harmonic potential (see Molecular dynamics parameters (.mdp options) — GROMACS 2018 documentation)