GROMACS version: 2023.3 with CUDA 12.3
GROMACS modification: No
Dear all,
I am trying to do umbrella sampling on a particular lipid inside a lipid bilayer generated through CHARMMGUI. However, as a relatively new GROMACS user, I am having difficulties implementing the process through a .mdp file, which I have been studying based on the Lemkul Lab’s GROMACS Tutorial.
Here are the questions I have:

How do I specify a pull group, particularly the head group of one specific lipid? Would I select a subcomponent of the lipid during .ndx creation as opposed to the entire lipid, and how would I go about doing that?

Assuming we have selected the lipid to pull in the bilayer but it is not at the position I need it to be, is it possible to measure the distance from the lipid to the center of the bilayer and move/pull/place it there before conducting umbrella sampling? i.e., I would like to move the lipid from the upper leaflet to the middle of the bilayer, then begin pulling upward.

Does the following .mdp (modified from Dr. Lemkul’s) for this purpose look appropriate overall?
Here, ‘TEST_LIPID’ would be defined according to our first question:
title = Umbrella pulling simulation
define = DPOSRES_B
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 250000 ; 500 ps
nstcomm = 10
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout = 500 ; every 1 ps
nstenergy = 500
; Bond parameters
constraint_algorithm = lincs
constraints = allbonds
continuation = yes ; continuing from NPT
; Singlerange cutoff scheme
cutoffscheme = Verlet
nstlist = 20
ns_type = grid
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = NoseHoover
tc_grps = MEMB SOLV
tau_t = 1.0 1.0
ref_t = 310 310
; Pressure coupling is on
Pcoupl = ParrinelloRahman
pcoupltype = semiisotropic
tau_p = 1.0
compressibility = 4.5e5
ref_p = 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Longrange dispersion correction
DispCorr = EnerPres
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 1 ; one group
pull_group1_name = TEST_LIPID
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 = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 1000 ; kJ mol^1 nm^2
Thank you in advance!