------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 12/15/2008 at 18:52:43 [-O]verwriting output File Assignments: | MDIN: min_wat.in | MDOUT: peg5k_wat_min_vac.out |INPCRD: peg5k_wat.crd | PARM: peg5k_wat.top |RESTRT: peg5k_wat_min_vac.rst | REFC: peg5k_wat.crd | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: water minimization &cntrl imin=1, ntmin=1, nmropt=0, maxcyc=2000, ncyc=500, drms=0.1 ntx=1, irest=0, ntpr=500, ntwr=500, iwrap=1, ntf=1, ntb=1, cut=8.0, nsnb=10, igb=0, ibelly=0, ntr=1, restraint_wt=300.0, restraintmask=':PEG' &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MPI getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read | peek_ewald_inpcrd: Box info found |Largest sphere to fit in unit cell has radius = 92.438 | New format PARM file being parsed. | Version = 1.000 Date = 12/11/08 Time = 17:10:40 NATOM = 673130 NTYPES = 6 NBONH = 672791 MBONA = 338 NTHETH = 1128 MTHETA = 337 NPHIH = 1572 MPHIA = 672 NHPARM = 0 NPARM = 0 NNB = 900394 NRES = 224226 NBONA = 338 NTHETA = 337 NPHIA = 672 NUMBND = 6 NUMANG = 8 NPTRA = 7 NATYP = 6 NPHB = 1 IFBOX = 1 NMXRS = 7 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 45186839 | Hollerith 4263008 | Integer 14652085 | Max Pairs 112188333 | nblistReal 8077560 | nblist Int 28791738 | Total 1040718 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 1, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 500, ntrx = 1, ntwr = 500 iwrap = 1, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 1, igb = 0, nsnb = 10 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 1 Energy minimization: maxcyc = 2000, ncyc = 500, ntmin = 1 dx0 = 0.01000, drms = 0.10000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 0 Box X = 210.514 Box Y = 189.075 Box Z = 184.875 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 216 NFFT2 = 192 NFFT3 = 192 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES Mask :PEG; matches 791 atoms -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 224113 | Atom division among processors: | 0 336566 673130 Sum of charges from parm topology file = -0.00000002 Forcing neutrality... | Running AMBER/MPI version on 2 nodes -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --------------------------------------------------- APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION using 5000.0 points per unit in tabled values TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 64334874 | TOTAL SIZE OF NONBOND LIST = 130571829 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -2.0718E+06 1.2878E+01 4.6876E+01 O 255546 BOND = 11.9930 ANGLE = 11.9798 DIHED = 149.6658 VDWAALS = 255264.3335 EEL = -2327043.6704 HBOND = 0.0000 1-4 VDW = 74.6611 1-4 EEL = -242.9567 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 500 -2.6553E+06 9.0453E-01 4.5365E+00 H1 309670 BOND = 182772.6607 ANGLE = 12.0148 DIHED = 149.6630 VDWAALS = 382962.1185 EEL = -3220992.9817 HBOND = 0.0000 1-4 VDW = 74.5605 1-4 EEL = -242.9492 RESTRAINT = 0.1223 EAMBER = -2655264.9134