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 CHARMM-GUI. 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?
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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.
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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 = all-bonds
continuation = yes ; continuing from NPT
; Single-range cutoff scheme
cutoff-scheme = 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 = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = Nose-Hoover
tc_grps = MEMB SOLV
tau_t = 1.0 1.0
ref_t = 310 310
; Pressure coupling is on
Pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range 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!