# Plop Molecular Dynamics

### From Jacobson Lab Wiki

**Dyn** is a top level plop command used to perform molecular dynamics simulations.

Control Words:

All normal commands for selecting residues are active

dyn [residue selection] & tempi [real] - sets the temperaure for the dynamics, and the initial temperature if annealing tempf [real] - sets the final temperature if performing annealing vinit [int] - controls how the initial energies are generated. vout [logical] - print out velocities at the end nbup [int] - frequency of neighborlist updates gbup [int] - frequency of GB alpha updates out [pdb/xyz] [filename] [int] - structure output type, output file, and frequency of output (in steps). rep [filename] [int] - dynamics information output file, and frequency of output (in steps). nsteps [int] - number of dynamics steps isot [option] - 'berend' = Berendsen thermostat, 'andersen' = Andersen thermostat, 'massive' is the massive stochastic collision version of Andersen, 'lange' is Langevin dynamics. taut [real] - Berendsen thermostat relaxation parameter / Andersen reassignment time dt [real] - time step length, in ps multi_num [int] - the number of short time scale time steps (with the short range potential) in beteen the long time scale steps, using respa verb [logical] - verbose output lange [logical] - use langevin dynamics friction [real] - langevin friction term parameter, in g/mol/ps fgh_update [int] - the type of force updating to use. Will usually be 111 or 112. 111 does not quite conserve energy, so won't work with isothermal (and may not be very good without sufficiently large cutoffs in general. dynend - exit from the routine, going back a level mon - calling Monte Carlo routines in mc.F that are not fully filled out right now.