SPARK MD

2. Molecular Dynamics Simulations

Input Files

Running a basic SPARK MD simulation requires a program executable (typically spark) that can access the input from four main input files: mol.inp, mol.xyz, mol.ff, and Periodic_Table.csv. The Periodic_Table.csv file contains basic atomic data, e.g. atomic mass, that normally does not have to be changed to run a simulation. Thus, to set up an MD simulation typically involves setting up or modifying existing version of the files mol.inp, mol.xyz, and mol.ff.
Once suitable input files have been constructed, the MD simulation can be run as ./spark > filename.out which generates several output files including the filename.out output file as well as separate trajectory files for structures (trj.xyz) and energy as function of time (trj_tE.csv).

mol.inp

The MD simulations are largely controlled by a number of parameters with default values that can be modified as line items in the mol.inp file.

Keyword	Type	Default	Options	Comment
#				Comment
system	int	0: Single Point		Atomistic Cell
runtype	int	0	1: Opt, 2: MD
simulation	int	1: NVT	0: NVE
timesteps	int	10000
timestep	double	0.01		unit: fs
trj_freq_update	int	100
start_velocity	double	0.01		unit: A/fs
temperature	double	300.0		unit: K
temp_response	double	0.0001		T equilibration rate. unit: K/fs
cell_boundaries	6 * double	3*(-10.0,10.0)		unit: A

mol.xyz

Atomic coordinates in simple csv-format with one atom per line (N,x,y,z).

Example: CO
C, 0.00, 0.00, 0.00
O, 0.00, 0.00, 1.20

mol.ff

Force Field specifying inter-atomic interactions (bonds, angles, dihedrals, etc).
Each line provides text-based information in csv-format about one force term according to a standard format with an ID, a list of objects and a list of associated parameters. Currently takes up to 8 objects and 12 parameters for each force specification.

ID, [objects], [parameters]

Example

Output Files

filename.out

Direct output reporting on progress of SPARK MD simulation in plain text format.

REMARKS:
1. NOTICE: This file is overwritten during restarts specifying the same output filename.
2. NOTICE: This file can get extremely large for long simulations as it currently by default displays key information for each MD cycle.

trj.xyz

The structural dynamics is captured in the trajectory file trj.xyz containing a series of atomic structures in simple Nxyz that can be visualized graphically using widely available molecule viewing software such as Avogadro (open file and select Extensions->Animation).

trj_tE.csv

The trj_tE.csv file details the simulation trajectory in terms of energy as a function of time. The data is collected in a csv format in which the first column lists the simulation time, the following several colums list different energy terms (bonds, angles, dihedrals, kinetic, etc as available) and the final column lists the total energy for each timestep.
The data output in the trj_tE.csv file can displayed in various ways including using dedicated Jupyter Notebooks or third party plotting and spreadsheet programs.