TUTORIAL 8 : Exercise 2

Water adsorption

In this exercise we will use GCMC to simulate water adsorption into a nano-pore.

Navigate to directory tutorial_8/slit-water

Check the FIELD file:

slit-water > more FIELD

The important points to note in the FIELD file are:

the energy unit is kJ/mol (real units)

ATOMS 3 3 and 3 lines that follow provide the molecule template (for GCMC)

EXCLUDE tells DL_MONTE not to include any intra-molecular interactions(!)

RIGID tells DL_MONTE to consider the molecule as a ‘rigid body’

VDW 3 shift implies 3 definitions for short-range interactions, truncated and shifted at cutoff(!)

the EXTERNAL wall-atom lj interactions are at play

epsilon = 9.0 kJ/mol and sigma = 3.2 Angstrom (from a wall) for OW atom type.

Check the CONTROL file:

slit-water > more CONTROL

The important directives to note in the CONTROL file are:

use gaspressure
use rotquaternion
use ortho

slit walls soft 2  #z-move -0.8
shifted damped 0.320

sample zdensity  500  1000

revconformat  dlpoly2
archiveformat dlpoly2+dcd

move gcinsertmol 1 50 2.5
SPCE 0.002

which instruct DL_MONTE to

use partial gas pressure in the GCMC (insertion/deletion)sampling;

use quaternion representation for molecule rotations;

use orthogonal variant of PBC (optimized for orthorhombic cells)

treat the system in a palnar slit geometry with two soft walls (not a 3D ‘slab’!)

employ a force-shifted and damped (truncated) variant of Coulomb interations (no Ewald!)

sample zdensity on a grid with 500 bins every 1000 MC steps (iterations)

store the REVCON file in both DL_MONTE (default) and DL_POLY-2 (additional) formats

store the trajectory in the following formats: dlpoly2 & dcd

perform GCMC moves (gcinsertmol) for 1 molecule type with weight 50(%) and min.distance = 2.5 A

the partial gas pressure for SPCE molecule is set to 0.002

Run the simulation and, when done, plot the density profile along z (ZDENSITY.000):

[tutorial_8]$ gnuplot
gnuplot> plot [x=-6:6] [y=0.:3.0] 'ZDENSY.000' u 1:2 w l t "Density(z)"

Questions to ask yourself:

  • How does the external potential look like?
  • How to increase or decrease the water adsoprtion? - What parameter(s) you could vary?
  • What will happen if you alter the external potential strength or distance?
  • What will happen if you alter the partial pressure for GCMC?
  • What will happen if you increase the cutoff radius?
  • What would be a good measure of the water adsorption?

If we increase the ‘steps’ number in CONTROL by a factor of 5 (uncomment the extra zero), we get slightly better results, as below.


Additional exercise:

Try to vary the external potential, and then partial pressure (gradually) and see the effect. Use VMD to visualise the trajectories.

Previous exercise:

TUTORIAL 8 : Exercise 1 - Ideal gas partitioning in a planar pore