Plop Molecular Dynamics

From Jacobson Lab Wiki

Revision as of 20:37, 26 January 2012 by Jbylund (Talk | contribs)
(diff) ←Older revision | Current revision (diff) | Newer revision→ (diff)
Jump to: navigation, search

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.
Personal tools