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

[Justin Lemkul]

On 2/28/19 2:09 PM, Javad Deylami wrote:
> 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)?

In principle, they can all be used to achieve equivalent results, though 
the cylinder geometry is largely designed for membranes and is described 
in detail in the manual.

> 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?

The alignment has nothing to do with the pull code. It means the initial 
coordinates should be aligned such that your reaction coordinate is 
coincident with the z-axis. For a typical lipid membrane, the membrane 
normal is already aligned along z since the membrane is in x-y. Then you 
just place your molecule of interest directly above the membrane.

-Justin

> 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.

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================