MolecularDynamics

Very simple molecular dynamics model. Currently attempts to implement a simplified version of the GAFF force field (e.g. no different atom environments). Has Andersen and Langevin thermostat kind of implemented, but Langevin doesn't really work.

Todo

• Fix units and get thermal control working
• Implement TIP3P water model
• Add the ability to have different models (e.g. define water and the molecule separately so bonding can be done)
• Different bond lengths for different atoms

Compilation

gcc main.c -lm -fopenmp -o md -O3

May be compiled with or without OpenMP support (this parallelises the atom loop).

Operation

The user interface is as in ThatPerson/Conformation. In scripting mode (eg ./md script.r) the following commands are implemented

• open <filename> Opens XYZ file <filename>
• bond <bl A> Introduced bonds between all atoms less than <bl A> apart (in Angstrom)
• output <filename> Writes XYZ file output into <filename>
• model <model> Sets up model <model>. Currently only <model> = MM3 is allowed.
• energy Prints out the energy of the system calculated using the forcefield.
• minimize <dn> <dt> <steps> <outputsteps> <filename> Runs minimization (e.g. velocity deleted each cycle, so system bond lengths and angles are relaxed) for <steps>, writing out the system to <filename> every <outputsteps>. Differentiation of the forcefield is done using <dn>, where this is a distance in Angstroms (generally ~0.01). Each step is <dt> picoseconds (generally 0.01).
• heat <temperature> <temp_step> <steps> <dn> <dt> <dnM> <dtN> <viscosity> <filename> Increments the temperature by <temp_step>, jumps forward <dn> <dt>, then runs minimization for <steps> with dn=<dnM> and dt=<dtN>. Repeats this until the tempeature reaches <temperature>
• iterate <dn> <dt> <temp> <viscosity> <filename> Jumps forward <dn> <dt>, allowing for more coarse iteration.
• hybridize <id> <sp> Changes atom hybridization state. This changes the expected bond angles. Atom ID is counted from XYZ file, indexed at 0. <sp> may be SP, SP2, or SP3 depending on site.
• prod <dn> <dt> <temperature> <viscosity> <step> <outputstep> <filename> Runs production MD. All inputs are as in minimize, except for <temperature> (see warning) and <viscosity> (see warning).
• temperature Outputs current system temperature
• thermostat <thermostat> <thermostat> can either be ANDERSEN or LANGEVIN. LANGEVIN is currently broken, see warning. With ANDERSEN temperature control seems okay but can explode. In ANDERSEN mode, the v parameter is taken from viscosity.