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Sander: 4. MD at 300 K / 1 atm (NPT)<br />
• 4-eq-density.inp:<br />
EQUILIBRATION ACETONE: DENSITY EQUILIBRATION<br />
&cntrl<br />
NPT canonical ensemble <br />
imin=0,<br />
! DEFAULT: Molecular Dynamics<br />
to adjust the density to <br />
! Nature and format of the input<br />
the equilibrium value of <br />
ntx=5,<br />
! Coordinates and velocities are read<br />
! formatted, box info is read if ntb>0 ≈ 1g/cm 3 . <br />
irest=1, ! Restart calculation (requires velocities in .rst file)<br />
...<br />
! Potential function<br />
ntf=2, ! Bond interactions involving H-atoms omitted<br />
ntb=2, ! Periodic boundary conditions with constant pressure<br />
cut=10.0, ! Non Bounded cutoff in Angstrom (DEFAULT 8.0)<br />
! frozen on restrained atoms<br />
ntr=0, ! DEFAULT: No position restraint<br />
! Molecular dynamics<br />
nstlim=300000, ! MD steps<br />
300000 • 1 fs = 300 ps = 0.3 ns <br />
dt=0.001, ! DEFAULT: Time step<br />
! Temperature regulation<br />
ntt=3, ! Langevin dynamics thermostat NPT canonical ensemble <br />
gamma_ln=1.0, ! Collision frequency of Langevin dynamics<br />
ig=71277, ! DEFAULT: Seed for pseudo number generator<br />
temp0=300.0, ! Reference temperature<br />
! Shake bond length constraints(only for MD)<br />
ntc=2, ! Bonds involving hydrogens are constrained<br />
! Pressure regulation<br />
ntp=1, ! Isotropic position scaling for constant pressure dynamics<br />
pres0=1.0, ! DEFAULT: Reference pressure (in atm)<br />
taup=2.0<br />
! Pressure relaxation time (in ps)<br />
/
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