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Sander: 1. Restrained Minimization<br />
• 1-restraint.inp:<br />
EQUILIBRATION ACETONE: RESTRAINT<br />
&cntrl<br />
imin=1, ! Minimization (Default: imin=0 MD run)<br />
irest=0, ! DEFAULT: No restart<br />
blank <br />
char. <br />
requ. <br />
here <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=1,<br />
! Position restraints (DEFAULT 0 = off)<br />
/<br />
/ concludes &cntrl namelist <br />
Restraints on Acetone<br />
500.0<br />
restraining specified atoms in cartesian space using harmonic poten4als <br />
RES 1<br />
• restraintmask string determines restrained atoms <br />
END<br />
END<br />
• restraint_wt force constant (k in kcal/mol; restraint = k • (x 2 ) <br />
• coordinates are read in „restr“ format from the refc file (contains all <br />
atoms); constrained atoms have to be specified. <br />
• Results: eq_restraint.out, *.rst, *.info<br />
NSTEP ENERGY RMS GMAX NAME NUMBER<br />
9899 -1.4707E+04 3.3717E-02 8.8112E-01 O 3056<br />
(ntb=2<br />
constant pressure) <br />
BOND = 1236.8131 ANGLE = 0.2058 DIHED = 4.7658<br />
VDWAALS = 3658.4484 EEL = -19568.1735 HBOND = 0.0000<br />
1-4 VDW = 0.4341 1-4 EEL = -39.7447 RESTRAINT = 0.0772<br />
EAMBER = -14707.2511
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