Essential Dynamics/Molecular Dynamics (EDMD) is a method developed by the Laughton group in Nottingham for efficient simulation of biomolecules. Rather than computing forces using a classical force-field on an atomistic level as per conventional Molecular Dynamics, EDMD treats sections of the biomolecule such as DNA tetrads as a single entity (coarse-graining), computes forces on each body independently based on a simplified force-field, and then integrates Newton's equations of motion in a reduced space spanned by the Principal Components of the motion (i.e. capturing the Essential Dynamics rather than the full atomistic Molecular Dynamics).

Two implementations of the EDMD method exist: A serial Python code with poor performance and a parallel Fortran 95/MPI code which lacks of the flexibility. The aim of the project is to evaluate the two existing codes, then implement a new version which combines the best of both worlds: a flexible parallelisation scheme to achieve good load balance on ARCHER, and the improved integrator and user interface from the Python code.

1. ./src : The folder contains all the source code inside;
2. ./test: The folder with two testing input file: the coordinate file and the tetrad parameter file;
3. ./data: The folder where the simulation results will be stored.
4. "config.txt" : The configuration file contains parameters to be initialised before the ED/MD simulation starts;
5. "Makefile" : The Makefile to compile the code on ARCHER;
6. "README.md" : The simple instruction of this code.
7. "edmddna.pbs": The script to submit the job to the back end of ARCHER

1. To compile the code on ARCHER, just type the command at the code directory: make.

2. To run the code on the back end of ARCHER, the code needs to be submitted: qsub edmddna.pbs

1. The QCP rotation calculation method in src/qcprot/. Developed by
   
   Douglas L. Theobald (2005), "Rapid calculation of RMSD using a quaternion-based characteristic polynomial.", Acta Crystallographica A 61(4):478-480.
   
   Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald (2009), "Fast determination of the optimal rotational matrix for macromolecular superpositions.", in press, Journal of Computational Chemistry

2. The random number generator in calculate_Random_Forces(Tetrad* tetrad) in src/edmd.cpp
   
   Adapted from the following Fortran 77 code: ALGORITHM 712, COLLECTED ALGORITHMS FROM ACM. THIS WORK PUBLISHED IN TRANSACTIONS ON MATHEMATICAL SOFTWARE, VOL. 18, NO. 4, DECEMBER, 1992, PP. 434-435.
   
   The function returns a normally distributed pseudo-random number with zero mean and unit variance. The algorithm uses the ratio of uniforms method of A.J. Kinderman and J.F. Monahan augmented with quadratic bounding curves.