Tutorial - use VMD Tcl/tk scripting to analyze a three-phase interface (water/oil/surface)

Concept scheme: left, free droplet; right, adsorbed droplet.

Example 1: calculate the amount of oil atoms on surface (within 0.36 nm)

This calculation is based on the center-of-mass (COM) distance between the atoms of the oil molecules and the atoms of surface molecules.

0. Download VMD software https://www.ks.uiuc.edu/Research/vmd/
1. Load the trajectory file in VMD; (e.g. wkpod300-comp.gro, drag the file to VMD Main or on VMD Main click File tab then New Molecule ...)
2. Open VMD TkConsole; (click Extension tab then Tk Console)
3. Set directory to the location of script file; (Use command "cd" and "cd .." to navigate and "pwd" to show current directory)
4. Type "source ott-count.txt" to execute the script and the data will be saved as "count_out.txt".

Output file is formated as <frame number> <counts>. (delimited by space)

Output example

0 0
1 106
2 198
3 211
4 213
5 230

File description:

oct-count.txt: Tcl script for counting numbers of non-polar oil atoms (resname OCT) within 3.6 Angstroms of kerogen surface (resname KER)
ott-count.txt: Tcl script for counting numbers of polar oil atoms (resname OTT) within 3.6 Angstroms of kerogen surface
wkpod300-comp.gro: gromacs trajectory file (six frames) of a polar oil cluster (30 octanethiols) interaction with a kerogen surface

Example 2: calculate the surface area (SA) of oil droplet

Solvent-accessible surface area method uses a imaginative sphere with a given probe radius (e.g. 0.14 nm) to measure the surface area of a selected region(s).

Courtesy of Keith Callenberg from Wikipedia

0. Download VMD software https://www.ks.uiuc.edu/Research/vmd/
1. Load the trajectory file in VMD; (e.g. wkpod300-comp.gro, drag the file to VMD Main or on VMD Main click File tab then New Molecule ...)
2. Open VMD TkConsole; (click Extension tab then Tk Console)
3. Set directory to the location of script file; (Use command "cd" and "cd .." to navigate and "pwd" to show current directory)
4. Type "source ott-sasa.txt" to execute the script and the data will be saved as "sasa_out.txt".

Output file is formated as <frame number> <total SA of oil> <contact SA of water/oil> < contact SA of surface/oil>. (delimited by space)

Output example

0 2889.4345703125 2848.1982421875 262.49859619140625
1 3706.266357421875 2836.384033203125 975.4174194335938
2 4283.4658203125 2657.725830078125 1629.1090087890625
3 4248.119140625 2598.83251953125 1571.08984375
4 4459.04833984375 2660.631103515625 1747.8780517578125
5 4613.27392578125 2723.780517578125 1727.9306640625

unit: angstrom²

File description:

oct-sasa.txt: Tcl script for analyzing surface area of a non-polar oil droplet.
ott-sasa.txt: Tcl script for analyzing surface area of a polar oil droplet.
wkpod300-comp.gro: gromacs trajectory file (six frames) of a polar oil cluster (30 octanethiols) interaction with a kerogen surface

Reference

arXiv preprint https://arxiv.org/abs/2007.09741
Wikipedia https://en.wikipedia.org/wiki/Accessible_surface_area
>>>>>> CC BY 4.0 <<<<<<