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NeutralDynamicsNeutral Dynamics sample input 60 ns neutral dynamics (NEUTRAL) &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 = 5000, ! 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, ! 2 periodic boundaries for constant pressure nstlim = 30000000, ! number of MD steps to be performed (60ns) dt = 0.002, ! 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=':1,6-12,17-22,32-45,52-64,74,77-87,105-121,142-163,176-183,196,199-221, 224-229,247-255,270-287,290-319,331-345,363-369,390-400,416-419,431-443,453-460, 469-479,490-494', / &end &wt type='END', &end Neutral Dynamics Output x_nd_#.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_nd_#.rst -- Single frame containing the atomic coordinates at the end of the simulation -- Can be used to restart or extend the simulation by specifying it as the -c file in the call to Amber mdcrd_nd_# -- 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 -- Used for analysis with cpptraj mdinfo_nd_# -- Contains an estimate of the amount of time remaining for neutral dynamics Path to Input Files
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