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Although our system has now been energy minimized, it is still a static structure. In the heating step, the system is gradually brought from a frozen 0K to 300K. This is implemented by randomly assigning velocities to each atom based on the Boltzmann distribution, putting the "dynamics" in "molecular dynamics." Because the velocities are assigned stochastically every time heating begins, this is the branching off point for individual independent MD runs. For a given experimental run, the velocities are inherited as one transitions through the protocol (from heating to equilibration to piggybacking - if needed - to production dynamics).

Because a computer cannot do continuous calculations, the Verlet algorithm is used to discretize into timesteps of 1-2 femtoseconds. In this way, the position of each atom can be updated at each timestep for however many timesteps the simulation is run. This process requires an initial velocity assignment that is stochastic and based on the Boltzmann distribution.

NOTE: Heating, equilibration, and neutral dynamics all use GPUs. They can be submitted as a single script, with the option of running several experiments as a part of the same job.

Heating sample input

   heating: MD with restraint on molecule
    &cntrl
     imin=0,		! no minimization
     irest=0,		! randomly assign velocities
     ntx=1,		! randomly assign velocities
     ntb=1,		! periodic boundaries for constant volume
     cut=10,		! non-bond cutoff of 10 angstroms
     ntr=1, 		! restraints on
     ntc=2, 		! SHAKE on
     ntf=2,		! bond interactions involving H omitted
     tempi=0.0,	        ! initial temperature
     temp0=300.0,	! ref temperature
     ntt=3, 		! Langevin dynamics
     gamma_ln=1.0,	! collision frequency
     nstlim=10000,      ! number of MD steps to be performed (20ps)
     dt=0.002,		! timestep in ps
     ntpr=1000, 	! print energy every 'ntpr' steps
     ntwx=1000, 	! write coord to trj every 'ntwx' steps
     ntwr=10000,	! rewrite rst file every 'ntwr' steps
     restraint_wt=20.0,
     restraintmask=':1 - 494'
 /

Heating output

  x_heat_#.out -- A summary of the system's energy printed incrementally
               -- This file will include information about the run timing at the bottom if the job ran to completion
               -- If the bottom of the file is energy information, the job is either still running or has crashed
  x_heat_#.rst -- Single frame containing the atomic coordinates at the end of the simulation
               -- Used as the starting structure for equilibration
  mdcrd_heat_# -- The trajectory containing a sampling of the coordinate frames of the simulation
               -- VMD can be used to step through the simulation and watch it back as a movie

Paths to Files

Input File:
/home66/kscopino/BIN/N2_SCRIPTS/20ps_heat.in

Master Python Script:
/home66/kscopino/BIN/N2_SCRIPTS/make_heat_equil_pb_dyn_scripts.py

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