vegadj/sumatra

#SUMATRA

A simple molecular dynamics engine driven by Langevin dynamics.

Sumatra is inspired by the molecular dynamic model as described in the paper:

JMB, 2003 H. Kaya, H. Chan (p. 911-931):

Solvation Effects and Driving Forces for Protein Thermodynamic and Kinetic Cooperativity: How Adequate is Native-centric Topological Modeling?

The emphasis is put on simplicity and robustness of developing a molecular dynamics simulation written in C. A full functional simulation can be expressed by a few core functions of Sumatra.

Building and Running

It's not rocket science.

git clone https://github.com/macoun/sumatra.git
cd sumatra
make

I've also included a demo pdb file to start right away. Run the demo simulation as follows.

./sumatra res/1cqu.pdb

Architecture

Module	Description
smtr.h/c	The Sumatra engine. The verlet algorithm and a small framework, which enables subscribing to events on trajectories and defining force fields, comprise the engine.
scg.h/c	The Sumatra Coarse Grain module implements the force fields as described in the reference paper.
vec3.h	You guessed it correctly! Another vector algebra library.

A schematic representation of a typical simulation application:

You can consider the SCG module as a helper or wrapper to smtr_add_force(). It also contains the update functions to the supported forces: stretching, bending, torsion, and nonbonded. It is seperated from the core Sumatra engine and can be replaced easily by your own force implementations.

Example

The following example shows how to setup a simluation and run it for 100k time steps at 0.5 simulation temperature.

void main()
{
	vec3 *particles = //...
	float *mass = //...
	int length = // length of particles and mass arrays

	smtr_init(particles, mass, length, 0.5);
	smtr_subscribe_event(print_event, NULL);
	
	scg_add_streching_force();
	scg_add_bending_force(20.0);
	scg_add_torsion_force(1.0, 0.5);
	scg_add_nonbond_force();
	  
	smtr_run_loop(100000);
}

For the sake of simplicity print_event() will print the coordinates of the 10th particle every 10000 steps.

int print_event(void *userData)
{
  vec3 *p;
  if (smtr_ctx->currentTimeStep % 10000 == 0)
  {
    p = smtr_ctx->particles + 10;
    printf("%3.7f %3.3f %3.3f\n", p->x, p->y, p->z);
  }
  
  // 0 means don't stop the simulation
  return 0;
}

What else

A random force as defined in Langevin dynamics will be added automatically if the simulation temperature is above zero.
Initial particle velocities are given randomly during initialization.
This is an ongoing project and I discourage using this in productive researches.

License

This version is licensed under MIT.

vegadj / sumatra