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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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