Analysing Results

This example shows how to use DL_ANALYSER to carry out post-analysis on the HISTORY file (or collection of the files). We intend to identify the type of hydrogen bond in the system by using the DANAI notation.

Step 1: DL_ANALYSER input file

  • Edit or create a DL_ANALYSER input file (e.g. dl_analyser.input), and insert all the pathnames for the HISTORY files for analysis. Make sure the pathnames to the HISTORY files are in the correct sequence.
../../_images/dl_analyser_input.png

In the above example, the file dl_analyser.input (found in the DL_ANALYSER directory workspace) was modified, and the HISTORY output files (from the DL_POLY MD runs) were already copied to the workspace/ETHANOIC_ACID_ANALYSIS/ directory.

Warning

Do not mix HISTORY files from different simulation models!

TIP:DL_ANALYSER can read the trajectory files in several formats: DL_POLY trajectory format (i.e. HISTORY), PDB, xyz and a mixture of all three, both in their respective native or compressed (gzip) formats, provided they were generated from the same simulation model.

Step 2: Edit the **DL_ANALYSER* control file (e.g. dl_analyser.control)*:

  • First of all, define a system to be analysed. This is located in the Atom Range Definition section. The number 5392 is the total number of atoms in the system.
  • The word ‘auto’ means DL_ANALYSER will determine the periodic boundary conditions based on the cell vectors from the trajectory files.
  • The Interaction Analysis Section is where the H-bond analysis is specified.
  • The test1.out is the formattable results output file.
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--- Atom Range Definition and overall conditions for analysis as below.
1 5392  * Range of atom index (Group A). This must always define.
none    * Range of atom index (Group B), if applicable. Or put 'none'.
1      * Analysis type: 1=atom-based  2 = molecule-base
acid  8    * Molecule-base analysis: name and no of atoms per molecule in Group A (MOLECULE A1)
none  * Molecule-base analysis: name and no of atoms per molecule in Group A (MOLECULE A2, or 'none')
none      * Molecule-base analysis: name and no of atoms per molecule in Group B (MOLECULE B1, or 'none')
none      * For molecule-base analysis: name and no of atoms per molecule in Group B (MOLECULE B2, or 'none')
all     * Range of MD time (ps) samples: t1  t2 (put 'all' if all samples to be included).
0    * Assign all atoms with unit mass = 1.0 (1=yes, 0=no)
auto   * Periodic boundary? 0=no, other number = type of box (DLPOLY), auto = obtain from HISTORY
28.320   0.000    0.0000  * Cell vector a (x, y, z)
0.000    21.95200 0.00000  * Cell vector b (x, y, z)
-2.0765488206    0.000 36.4008179166  * Cell vector c (x, y, z)
0        * Exclude any atoms for analysis? 0=no, any number = Number of EXCLUDE statements shown below.
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--- Interaction analysis (DANAI)
1              * Activate analysis (1=yes, 0=no)
test1.out       * Output file
0              * Number of every configuration to skip
1              * Consider intra-interaction (A-A, B-B)
0              * Consider inter-interaction (A-B)
2.5  120.0     * H-bond definition: distance, angle (donor-H---acceptor)
4.5            * Hydrophobic contact distance (between alkyl carbons)
4.5  15.0      * pi-pi aromatic stacking: distance between ring, Acute angle (max.) between ring planes
0              * Cross-correlation between TWO different interactions (only works if 2 interactions are selected)
0              * alkyl-alkyl interactions (HP_1_1)
0              * aromatic-aromatic (benzene rings) interactions (HP_6_6)
0              * alcohol-alcohol (OH-OH) interactions (HB_15_15)
0              * alcohol-carboxylic interactions (HB_15_20)
0              * alcohol-aniline interactions (HB_15_46)
1              * carboxylic-carboxylic interactions (HB_20_20)
0              * carboxylic-aniline interactions (HB_20_46)
0              * water-water (HB_800_800)
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Step 3: Edit dl_a_path file

  • Create the file dl_a_path in the workspace directory. Make sure the paths for the control and input files are correct.
../../_images/dl_a_path.png

Step 4: Run DL_ANALYSER

  • Within the workspace directory run dl_analyser

    $ ./dl_analyser

  • Upon successful execution, the dl_analyser.output file will be produced, highlighting the general analysis status and reading process. In addition, results output files will also be produced, depending on the dl_analyser.control file, in this example the results data file is test1.out. Below you can see the output to screen while the program is running:

../../_images/dl_analyser_output.png

Note

In the above output of DL_ANALYSER the time taken to set up neighbour lists is 0.684 s. It will take much longer if your system is large, although this is only a one-off process.

Step 5: Analysis results output

  • These results are given in a raw data format that needs to be extracted for further processing such as plotting a graph.
../../_images/dl_a_test1_out.png

The figure above shows the beginning (LHS) and end (RHS) of the data results file (in this example it’s test1.out).

  • The output file shows three different parts to the results:

    • Detection of various hydrogen-bond (HB) interactions modes between carboxylic groups with respect to MD time.
    • Average number of interactions for each mode.
    • Correlation coefficients among the interaction modes.