[gmx-users] Pulling ion across the bilayer-choosing pull_coord1_geometry
Javad Deylami
javaddeilami at gmail.com
Thu Feb 28 20:10:00 CET 2019
Hi Justin,
I have one general and one specific question about doing the pulling
simulation.
Can you let me know how I should choose pull_coord1_geometry among
distance, direction, and cylinder? How can I distinguish these three
geometries to use them in different systems? How can different choices
affect the outcome (PMF curve)?
Which methos you recomment to pull a molecule acroos the bilayer? why?
In my case, I want to calculate the permeability of ion in a specific
bilayer. I faced this error: Can not have dynamic box while using pull
geometry 'direction-periodic' (dim z)
I found you already replied the similar issue: *"align the system such that
you are pulling along z, in conjunction with semi-isotropic coupling and
zero compressibility along z."*
Can you explain how I should do that alignment in my pull code?
This is my pull code:
title = Umbrella pulling simulation
define = -DDPPC_O
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 500000 ; 1000 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 SOL_ION
tau_t = 1.0 1.0
ref_t = 303.15 303.15
; Pressure coupling is on
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 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
; Pull code
pull = umbrella
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction
coordinate
pull_group1_name = CAL
pull_group2_name = DPPC_O
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull-geometry = direction-periodic
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull-coord1-vec = 0 0 1
pull-coord1-init = 0 ;
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
Your attention is highly appreciated.
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