Ready, get set, go¶
This page tells you how to set DL_ANALYSER up and running.
How to obtain DL_ANALYSER
DL_ANALYSER – results analysis program.
DL_ANALYSER User Manual (
The DL_ANALYSER User Manual) - Version 2.2, March 2020.
To be able to use the latest version of DL_ANALYSER you first need to register here. Successful registration will lead to the receipt of an email with the latest version of DL_ANALYSER attached e.g. dl_a_2.2.tar.gz. Untar this file for example in Linux:
$: tar -xzvf dl_a_2.2.tar.gz
Note
The number 2.2 refers to the software version, which can be different if a newer version is released.
This will produce the DL_ANALYSER home directory dl_a_2.2. To compile the program, go to the source/ directory and type the command:
$: make
This will create the dl_analyser executable file in the directory called workspace.
General guidance for running DL_ANALYSER
The workspace/ directory is where all the neccessary support files are located. This is shown as follows:
dl_analyser.control - This is the default DL_ANALYSER control file. It can be renamed or copied.
dl_analyser.input - This is the default DL_ANALYSER input file where you insert the configuration or trajectory files. It can be renamed or copied.
atom_list_A and atom_list_B - Two special files that list the individual atom indices to be selected for analysis, They are referred to atoms from Group A and Group B, respectively.
dl_a_path - A file that indicates the directory paths and names of the DL_ANALYSER control and input files.
run_dla - A file script to run DL_ANALYSER program.
Before running DL_ANALYSER, make sure the paths for DL_ANALYSER control and input files are correct as shown in the dl_a_path below:
The example file dl_a_path above indicates both files are in the DL_ANALYSER home directory
Note
DL_ANALYSER always look for the file dl_a_path, which must be located in the same directory as the dl_analyser executable file (the DL_ANALYSER home directory).
DL_ANALYSER can read the trajectory files in several formats: DL_POLY trajectory format (HISTORY), PDB, xyz, DL_POLY CONFIG file and any mixture of these, both in their respective native or compressed (gzip) formats. In practice, it is more common to read a serial collection of HISTORY files generated from the same simulation models.
If your DL_ANALYSER cannot read the .gz file, you can use the uncompressed version of the file. A typical DL_ANALYSER input file (dl_analyser.input) is shown below:
Note
The number (n) at the start of the dl_analyser.input file (in the above example this is 3) instructs DL_ANALYSER to read only the first n lines, where it expects the path contains the input trajectory files. The program will ignore anything beyond that.
The DL_ANALYSER suite version 2.2 onward also comes with a simple run script called run_dla. If your program is compiled with the OpenMP library (by default), then type:
$ ./run_dla
This will run the DL_ANALYSER program using the specified number of OpenMP threads as shown in the run_dla script. You can change the value according to your preference. If you run the program by typing:
$ ./dl_analyser.exe
then the number of threads used for the OpenMP parallelisation will depend on the OS of your computer. The actual number will be reported by DL_ANALYSER when the program is run.
Example structures
The DL_ANALYSER software packages comes with a DL_POLY HISTORY example file called HISTORY_acetic.gz. All the supporting files, including the dl_a_path file are pre-set to analyse the trajectory file. It is a small ethanoic acid liquid MD trajectory file generated using DL_POLY.
Below shows the content of the dl_analyser.control file:
+…
…
…
--- 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.
…
…
…
--- 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)
…
…
…
The highlighted lines are examples of what you might want to change in the file, e.g.
The number 5392 is the total 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 results output file.
Note
All DL_ANALYSER runs will always produce a file called dl_analyser.output in the workspace/ directory, which reports the analysis status, and output files of the results according to what you specified in the DL_ANALYSER control file.
Now, type ./run_dla or ./dl_analyser and see what happens.