GROMACS version:GROMACS 2019.6
GROMACS modification: No
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I am actually trying to pull the AFM tip towards my multi-bilayer lipid membrane which is on a frozen surface. The tip is actually in vacuum and is position restraint. I have tried to consider PBC atom as bead at the tip of the triangular structure (AFM tip) and a bead from popc tail just opposite of the tip. But the tip didn’t move at all. Then I changed the PBC atom to -1 for both groups. And on doing that my POPC started detaching from the frozen surface and my tip didn’t move at all. Here is my pull.mdp file:
title = Umbrella pulling simulation
define = -DPOSRES
; Run parameters
integrator = md
dt = 0.01
tinit = 0
nsteps = 5000000
nstcomm = 100
; Output parameters
nstxout = 1000
nstvout = 1000
nstfout = 100
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
xtc_precision = 100
xtc-grps =
energygrps = SIO2 GRAP POPC
energygrp_excl = SIO2 SIO2 GRAP GRAP
; Bond parameters
constraint_algorithm = lincs
constraints = none
continuation = yes
lincs_order = 4
lincs_warnangle = 30
; Single-range cutoff scheme
cutoff-scheme = group
nstlist = 10
ns_type = grid
rlist = 1.4
rcoulomb = 1.2
rvdw = 1.2
; PME electrostatics parameters
coulombtype = Shift
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
;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 = berendsen
tc_grps = SIO2 GRAP POPC
tau_t = 1.0 1.0 1.0
ref_t = 298 0 298
; Pressure coupling is on
Pcoupl = no
pcoupltype = semiisotropic
tau_p = 1.0
compressibility = 0e-5 3e-5
ref_p = 0.0 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
freezegrps = GRAP
freezedim = Y Y Y
cos-acceleration = 0
; Pull code
pull = yes
pull_ncoords = 1
pull_ngroups = 2
pull_group1_name = SIO2
pull_group2_name = POPC
pull_group1_pbcatom = -1; 7522
pull_group2_pbcatom = -1; 57872
pull-pbc-ref-prev-step-com=yes
pull-coord1-vec = 0.0 0.0 1.0
pull-coord1-init = 1
pull_coord1_type = umbrella
pull_coord1_geometry = direction-periodic
;pull_coord1_r = 5.0
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = yes
pull_nstxout = 100
pull_nstfout = 100
pull_coord1_rate = -0.001
pull_coord1_k = 1000
After this, I considered putting a position restraint on the popc lipids in the z-direction and removing the position restraint on the tip in the z-direction. But in thin that case my tip lost its shape therefore I put back the z-restraint again. And now I am trying to run by having my tip position restraint and the lipid is restraint only in the z-direction, but still, my tip is not getting pulled down and my lipids somehow are coming down. Can you please help me with this. Thank you so much for your time and consideration.
Looking forward to hearing from you.
Best,
Saswati