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Sander: 3. MD heating to 300 K<br />
EQUILIBRATION ACETONE: HEATING<br />
&cntrl<br />
imin=0, ! DEFAULT: Molecular Dynamics<br />
! Nature and format of the input<br />
ntx=1,<br />
irest=0, ! DEFAULT: No restart<br />
! Nature and format of the output<br />
ntpr=200, ! Steps for energy info in .out and .info<br />
ntwr=1000, ! Steps for restart file (.rst)<br />
ntwx=500, ! Steps for coordinates file (.crd)<br />
ntwe=500, ! Steps for energy file (.en)<br />
! Potential function<br />
ntf=2,<br />
! coordinates are read formatted / no initial velocities<br />
! Bond interactions involving H-atoms omitted<br />
! (use with ntc=2)<br />
longer dt possible <br />
ntb=1,<br />
! DEFAULT: Periodic boundary conditions with constant volume<br />
cut=10.0, ! Non Bonded cutoff in Angstrom (DEFAULT 8.0)<br />
! Frozen on restrained atoms<br />
ntr=1,<br />
! Position restraint<br />
! Molecular dynamics<br />
300.000•1fs = 300 ps = 0.3 ns <br />
nstlim=300000, ! MD steps (at least > 10 ps, the relaxation time of water)<br />
dt=0.001, ! DEFAULT: Time step (in ps: 0.001 ps = 1 fs) dt should be one <br />
! Temperature regulation order of magnitude smaller than the fastest process (rot./vib.) <br />
ntt=3,<br />
! Langevin dynamics thermostat<br />
NVT canonical ensemble <br />
gamma_ln=1.0, ! Collision frequency of Langevin dynamics<br />
ig=71277, ! DEFAULT: Seed for pseudo number generator:<br />
! change it at each restart!<br />
...<br />
temp0=300.0, ! Reference temperature<br />
tempi=0.0, ! Initial temperature<br />
• 3-heating.inp:<br />
X-‐H DOF have lible <br />
influence on many <br />
proper4es: <br />
room temperature <br />
ini4al veloci4es calculated from forces (if 0) <br />
or from a Maxwell distribu4on at T=0K
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