Solution model analysisΒΆ

Below lists a number of simulation trajectories produced from DL_POLY. By using these as input structures, D_ATA can analyse and identify atomic interactions present in the systems.

Note that since they are of different systems, each can only be analysed one at a time.

  1. Acetone in water (xyz format). A system model consist of 30 acetone (propanone) molecules in water to give a total of 6408 atoms. Atom index 1 to 300 belongs to the 30 acetone molecules. Atom index 301 to 6408 belongs to water molecules.
  2. Pure pentanoic acid liquid (xyz format). A system model consists of 2808 pentanoic acid molecules, with a total of 47736 atoms.
  3. Ethylacetate in water (DL_POLY trajectory). Twenty ethylacetate molecules dissolve in 2040 water molecules. Atom index 1 to 280 belongs to the organic molecule and atom index 281 to 6400 belongs to water molecules.
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Procedures

  1. Compile D_ATA program.
  2. Select and download trajectory file. Save the file to your D_ATA home directory (where d_ata executable file is located).
  3. Edit and insert the filename of the downloaded trajectory file in d_ata.input, as shown below:
# Since there is only one file and hence the number 1.
1
XXX

where XXX is the filename of the downloaded trajectory. For example, acetone_water.xyz.gz. If your trajectory file is located in other folder, then remember to specify the path as well.

If your D_ATA version cannot read the gzip compressed file, then use gunzip to uncompress it and change the filename accordingly.

Save and exit d_ata.input.

  1. Edit and view the d_ata.control file. Select the options as shown below:
Title for control file.
2              * Program mode: 1=typer, 2=typer and analyser.
0              * All-inclusive interaction mode (1=yes, 0=no).
none           * PDB, gro, d_ata.template or 'none'
auto           * Periodic boundary condition type
40.0 0.0 0.0   * Cell vector a (x, y, z)
0.0 40.0 0.0   * Cell vector b (x, y, z)
0.0 0.0 40.0   * Cell vector c (x, y, z)
all           * Group A: Atom range. Min Max or 'all'
1              * Molecule-based analysis (0 = off, 1=betwen molecule, 2=within molecule).
2              * No of configuration to skip
1              * DANAI tier level.
0.002          * Average count fraction threshold
2.5            * Distance threshold for H...D in HB interactions
120.0          * Angle threhold for HB interactions
4.5            * Distance threshold for C...C in HP interactions
1              * HB analysis
1              * HP analysis

Save and exit d_ata.control.

  1. Run D_ATA program at the home directory by simply type ./d_ata
  2. Upon finish running the analysis, the following files will be produced in the OUTPUT_PATH folder:
  • d_ata.output
  • d_ata.csf
  • d_ata.results
  • A number of count-time profile files (count_XXX.results), if any. See d_ata.results for details.
  1. Change control options such as number of atoms to analysis, analysis criteria, etc and rerun D_ATA.

Please refer to manual or D_ATA reference guide for more information on how to interpret output results.

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