MD options

Molecular dynamics simulations are invoked with the turbogap md command. The most important options in the input file that you need to worry about are:

1. md_step: the time step for velocity Verlet integration;
2. md_nsteps: the number of time steps to propagate the atomic positions;
3. thermostat: formalism to keep the temperature constant (or not);
   1. t_beg: the initial thermostating temperature if a thermostat is chosen;
   2. t_end: the final thermostating temperature if a thermostat is chosen;
   3. tau_t: the time constant for the thermostat, if chosen;
4. barostat: formalism to keep the pressure constant (or not);
   1. p_beg: the initial barostating pressure if a barostat is chosen;
   2. p_end: the final barostating pressure if a barostat is chosen;
   3. tau_p: the time constant of the barostat, if chosen;
   4. gamma_p: the inverse compressibility of the system if a thermostat is chosen;
   5. barostat_sym: selects which degrees of freedom of the simulation box are affected by the barostating;
5. scale_box: determines whether the simulation box is scalend during the simulation;
6. box_scaling_factor: determines by how much the box will be increased during the simulation;
7. write_thermo: how often to write out thermodynamic information;
8. write_xyz: how often to write out detailed trajectory information;
9. write_lv: determines whether the lattice vectors are written together with the thermodynamic information;
10. neighbors_buffer: defines a buffer region beyond the potential's actual cutoff to enable less frequent neighbor list builds.