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EquilibrationEquilibration sample input 3ns equilibration step (EQUIL) &cntrl imin = 0, ! no minimization ntx = 5, ! velocities inherited irest = 1, ! velocities inherited ntpr = 5000, ! print energy info every `ntpr` steps ntwr = 50000, ! rewrite rst file every `ntwr` steps ntwx = 1000, ! write coord to trj every `ntwx` steps ntf = 2, ! bond interactions involving H omitted ntc = 2, ! SHAKE on, Hbonds constrained cut = 8.0, ! non-bond cutoff of 8A ntb = 2, ! periodic boundaries for constant pressure nstlim = 3000000, ! number of MD steps to be performed (3ns) dt = 0.001, ! time step in psec tempi = 0.0, ! initial temperature temp0 = 300, ! ref temperature ntt = 3, ! Langevin dynamics gamma_ln = 1.0, ! collision freq ntp = 1, ! constant pressure dynamics pres0 = 1.0, ! reference pressure 1 taup = 5.0, ! time constant for pressure nmropt = 1, ! restraint on ioutfm = 1, ! write binary trajectory ntr = 1, ! restraint on restraint_wt = 20.0, restraintmask=':1-494', / &end &wt type='END', &end Equilibration output x_equil_#.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_equil_#.rst -- Single frame containing the atomic coordinates at the end of the simulation -- Used as the starting structure for neutral dynamics (or piggybacking) mdcrd_equil_# -- 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 mdinfo_equil_# -- Contains an estimate of the amount of time remaining for equilibration Path to Input Files
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