Atomic Interaction Analysis Using D_ATAΒΆ

This page is related to the tutorial section to setup a solution model using DL_FIELD. If you have not done so, please go to Setup solutions.

If you have not run the simulation to produce the HISTORY trajectory file, please go to Run Simulation (DL_POLY).

Otherwise, continue on as follows:

We are now going to determine types of hydrogen bond (HB) interactions present in the system by using D_ATA to analyse the HISTORY file produced from the previous tutorial.

Procedures

  1. Edit D_ATA input file (d_ata.input) and insert HISTORY as the input file:
1
HISTORY
..
..

Close and save the file.

  1. Use this control file (d_ata.control) as shown below:
Title for control file.
2              * Program mode: 1=typer, 2=typer and analyser.
1              * 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).
1              * 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
  1. Run D_ATA by typing ./d_ata
  2. Inspect output files: d_ata.output and d_ata.results.

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