[gmx-users] Pulling ion across the bilayer-choosing pull_coord1_geometry

[Javad Deylami]

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.