DL_ANALYSER - A general analysis tool for DL_POLY. CCP5 Software

DL_ANALYSER

C W Yong - Scientific Computing Department, STFC, Daresbury Laboratory.

Latest version: 2.3 released September 2021

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What is new in Version 2.3

(1) Select analysis criteria for atom-based analysis: within molecules, between molecules or all atoms.
(2) Interaction Analysis Section: Detection for ammonium, carboxylate and water interactions. Detection for haloalkanes interactions.

(3) Biological Analysis Section: Allow non-amino acid for the phi-psi dihedral calculations

(4) Structural Analysis Section: Angular distributions between two non-bonded bond vectors.

(5) Dynamical Analysis Section: Velocity autocorrelation functions (VACF) and its Fourier Transforms.

(6) Additional general analysis features: reduced moments.

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DL_ANALYSER is a computer program package written in C that primarily serves as a support application software tool for DL_POLY molecular dynamics simulation package. DL_ANALYSER is developed at Daresbury Laboratory by C. W. Yong under the auspices of the Engineering and Physical Sciences Research Council (EPSRC) for the EPSRC's Collaborative Computational Project for the Computer Simulation of Condensed Phases (CCP5).

First released in May 2014, this is a software tool written in C to carry out a variety of post analysis work on the trajectory files produced by the DL_POLY molecular dynamics (MD) package. The program basically contains a collection of unified analysis tools that can produce a variety of results concurrently in a single-read through a collection of trajectory files. The nature and type of results to produce can be controlled in one single DL_ANALYSER's control (dl_analyser.control) file whereby the user just switches on or off to a selection of options. In addition, the analysis options can also be applied on a selection of atoms specified by the users.

Diagram below illustrates schematically how DL_ANALYSER functions:

The yellow boxes represent the DL_ANALYSER main program components. The dotted lines indicate the involvement of third-party packages where data adjustments may be needed for final results presentations and animation purposes. However, the output trajectory file is fully compatible with DL_ANALYSER, which can be carried out for repeat or further analysis.

Features:

Able to read file (compress or uncompress) in the following format: HISTORY, CONFIG, STATIS, PDB and xyz.
Able to write in the following format: PDB and xyz (from the trajectory files, for instance).
Applicable to the following molecular models: Pretty much anything, but can be depended on how a model is set up.
Structural analysis
Dynamical Analysis
Structural Defect Analysis
Surface Sputter Analysis
Biological analysis
Interaction analysis

The analysis software contains the unique feature whereby it can detect, quantify and annotate the various modes of atomic interactions, without the need of using pictorial or diagrammatic illustrations. This is achieved by making use of the DL_F Notation, implemented within the DL_FIELD program. From such, the DL_ANALYSER Notation for Atomic Interactions, DANAI, has been implemented. It is a natural expression system to annotate detailed, localised atomic interactions. For more details, please refer to the following reference:

C.W. Yong and I.T. Todorov, Molecules (2018), 23, 36 (doi:10.3390/molecules23010036)

DL_ANALYSER is supplied to individuals under an academic licence, which is free to academic scientists pursuing scientific research of a non-commercial nature. Please see the web page Registering for the DL_ANALYSER Package for instructions. Commercial organisations interested in acquiring the package should approach Dr. C. W. Yong at Daresbury Laboratory in the first instance. Daresbury Laboratory is the sole centre for distribution of the package.

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For more information, question, comment about DL_ANALYSER please contact Dr C W Yong