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Sander: 2. Unrestrained Minimization<br />
• 2-minimization.inp:<br />
EQUILIBRATION ACETONE: RESTRAINT<br />
&cntrl<br />
imin=1, ! Minimization (Default: imin=0 MD run)<br />
ntx=1,<br />
! coordinates are read formatted / no initial velocities<br />
irest=0, ! DEFAULT: No restart<br />
ntb=1,<br />
! DEFAULT: Periodic boundary conditions with constant volume<br />
cut=10.0, ! Non-Bonded (Coulomb+VDW) cutoff in Angstrom (DEFAULT 8.0)<br />
maxcyc=50000, ! Maximum number of cycles of minimization (DEFAULT 1)<br />
ncyc=300, ! Number of initial cycles using steepest descent method,<br />
! after ncyc: conjugate gradient(DEFAULT 10)<br />
ntr=0,<br />
! No position restraints (DEFAULT 0 = off)<br />
/<br />
• Results: eq_minimization.out, *.rst, *.info <br />
NSTEP ENERGY RMS GMAX NAME NUMBER<br />
5596 -1.4743E+04 5.8665E-03 1.0262E-01 H2 2080<br />
BOND = 1240.3048 ANGLE = 0.0822 DIHED = 4.8192<br />
VDWAALS = 3659.2696 EEL = -19608.3578 HBOND = 0.0000<br />
1-4 VDW = 0.5127 1-4 EEL = -39.9970 RESTRAINT = 0.0000
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