Biomodeling: DNA in a Nanopore

Intro

References


Hello, DNA!

Outputs from web server


Perform MD of dsDNA in solution

; Include forcefield parameters

#include "amber99bsc0.ff/forcefield.itp"


;#define POSRES

#include "dna.itp"

#include "dna.pbc.itp"

#include "dna.hbonds.itp"

;#include "posre.itp"

;#include "dna.enm.itp"


; Include water topology

#include "amber99bsc0.ff/tip3p.itp"


; Include topology for ions

#include "amber99bsc0.ff/ions.itp"


[ system ]

; Name

loop in water


[ molecules ]

; Compound        #mols

DNA_chain_A         1

SOL              7618


Add ions & minimize


MDRUN


; RUN CONTROL PARAMETERS

integrator               = md

; Start time and timestep in ps

tinit                    = 0

dt                       = 0.002

nsteps                   = 500000000


; Temperature coupling  

tcoupl                   = v-rescale

print-nose-hoover-chain-variables = no

; Groups to couple separately

tc_grps                  = system

; Time constant (ps) and reference temperature (K)

tau_t                    = 0.5

ref_t                    = 300

Because we have a dsDNA along the z axis, the box size in z must be decoupled from x and y sizes. Similar to the lipid bilayer systems, this DNA system fits best with semi-isotropic box.

; pressure coupling     

Pcoupl                   = c-rescale

Pcoupltype               = semi-isotropic

; Time constant (ps), compressibility (1/bar) and reference P (bar)

tau-p                    = 1.0

compressibility          = 4.5e-5 4.5e-5 

ref-p                    = 1      1



Analysis


# lines starting with "#" or "@" are comments.

# Each columns are time (ps)  x  y  z (nm)

 0      4.49242 2.58475 3.55809

 20     4.60075 2.66173 3.73794

 40     4.67276 2.70951 3.65495

 60     4.6117  2.61924 3.74992

 0      {x, y, z of ion 1}  {x, y, z of ion 2} ...

 20     {x, y, z of ion 1}  {x, y, z of ion 2} ...

 40     {x, y, z of ion 1}  {x, y, z of ion 2} ...

 60     {x, y, z of ion 1}  {x, y, z of ion 2} ...

...

Perform MD of dsDNA in a Graphene Nanopore (Not yet done)

Solvation

Minimization

md.mdp – Pressure coupling

; pressure coupling     

Pcoupl                   = berendsen

Pcoupltype               = anisotropic

; Time constant (ps), compressibility (1/bar) and reference P (bar)

tau-p                    = 1.0

compressibility          = 4.5e-5 4.5e-5 4.5e-5

ref-p                    = 1      1      1



md.mdp – Electric field


; Electric fields

; Format for electric-field-x, etc. is: four real variables:

; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps),

; and sigma (ps) width of the pulse. Omega = 0 means static field,

; sigma = 0 means no pulse, leaving the field to be a cosine function.

electric-field-x         = 0 0 0 0

electric-field-y         = 0 0 0 0

electric-field-z         = 0.142857 0 0 0



Perform MD

Visualizing ionic flow

Homework