------------------------------------------------------- Amber 6 SANDER Scripps/UCSF 1999 ------------------------------------------------------- | Thu Feb 17 16:06:22 2005 [-O]verwriting output File Assignments: |MDIN : 4col.min.in |MDOUT: 4col.out |INPCR: 4col.crd |PARM : 4col.top |RESTR: 4col.rst |REFC : 4col.crd |MDVEL: mdvel |MDEN : mden |MDCRD: mdcrd |MDINF: mdinfo Here is the input file: MINIMIZATION OF 3'HYDROXY PROLINE COLLAGEN &cntrl imin=1, maxcyc=20000, ncyc=0, ntmin=1, ntpr=500 &end ------------------------------------------------------------------------------- MINIMIZATION OF 3'HYDROXY PROLINE COLLAGEN 1. RESOURCE USE: getting box info from bottom of parm getting new box info from bottom of inpcrd | peek_ewald_inpcrd: Box info found EWALD SPECIFIC INPUT: | Using the SGI specific (ZFFT3D) Fast Fourier Transform ------------------------------------------------- NO EWALD INPUT FOUND: USING DEFAULTS ------------------------------------------------- Largest sphere to fit in unit cell has radius = 17.050 Calculating ew_coeff from dsum_tol,cutoff Box X = 34.207 Box Y = 34.100 Box Z = 117.032 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 36 NFFT2 = 36 NFFT3 = 120 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 NATOM = 7353 NTYPES = 12 NBONH = 6783 MBONA = 627 NTHETH = 1275 MTHETA = 921 NPHIH = 2250 MPHIA = 1917 NHPARM = 0 NPARM = 0 NNB = 14923 NRES = 2179 NBONA = 627 NTHETA = 921 NPHIA = 1917 NUMBND = 16 NUMANG = 29 NPTRA = 16 NATYP = 14 NPHB = 1 IFBOX = 1 NMXRS = 15 IFCAP = 0 EWALD MEMORY USE: | Total heap storage needed = 682 | Adjacent nonbond minimum mask = 14923 | Max number of pointers = 25 | List build maxmask = 29846 | Maximage = 10757 EWALD LOCMEM POINTER OFFSETS | Real memory needed by PME = 682 | Size of EEDTABLE = 20918 | Real memory needed by EEDTABLE = 83672 | Integer memory needed by ADJ = 29846 | Integer memory used by local nonb= 512166 | Real memory used by local nonb = 120507 | MAX NONBOND PAIRS = 5000000 | Memory Use Allocated Used | Real 2500000 602421 | Hollerith 600000 46299 | Integer 2000000 766877 | Max Nonbonded Pairs: 5000000 BOX TYPE: RECTILINEAR 2. CONTROL DATA FOR THE RUN TIMLIM= 999999. IREST = 0 IBELLY= 0 IMIN = 1 IPOL = 0 NTX = 1 NTXO = 1 IG = 71277 TEMPI = 0.00 HEAT = 0.000 NTB = 1 BOXX = 34.207 BOXY = 34.100 BOXZ = 117.032 NTT = 0 TEMP0 = 300.000 DTEMP = 0.000 TAUTP = 1.000 VLIMIT= 0.000 NTP = 0 PRES0 = 1.000 COMP = 44.600 TAUP = 0.200 NPSCAL= 0 NTCM = 0 NSCM = 9999999 NSTLIM= 1 NTU = 1 T = 0.000 DT = 0.00100 NTC = 1 TOL = 0.00001 JFASTW = 0 NTF = 1 NSNB = 25 CUT = 8.000 SCNB = 2.000 SCEE = 1.200 DIELC = 1.000 NTPR = 500 NTWR = 50 NTWX = 0 NTWV = 0 NTWE = 0 IOUTFM= 0 NTWPRT= 0 NTWPR0= 0 NTAVE= 0 NTR = 0 NTRX = 1 TAUR = 0.00000 NMROPT= 0 PENCUT= 0.10000 IVCAP = 0 MATCAP= 0 FCAP = 1.500 OTHER DATA: IFCAP = 0 NATCAP= 0 CUTCAP= 0.000 XCAP = 0.000 YCAP = 0.000 ZCAP = 0.000 VRAND= 0 NATOM = 7353 NRES = 2179 MAXCYC=20000 NCYC = 0 NTMIN = 1 DX0 = 0.010000 DXM = 0.50000 DRMS = 0.00010 Water definition for fast triangulated model: Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2 3. ATOMIC COORDINATES AND VELOCITIES begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 2089 Sum of charges from parm topology file = 0.00000015 Forcing neutrality... --------------------------------------------------- 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 = 0.2088E-14 at 2.598900 | CHECK d/dx switch(x): max rel err = 0.7671E-11 at 2.757160 --------------------------------------------------- Total number of mask terms = 12804 Total number of mask terms = 25608 | Total Ewald setup time = 0.21217823 ------------------------------------------------------------------------------ NSTEP ENERGY RMS GMAX NAME NUMBER 1 6.1081E+08 1.3472E+07 2.4186E+08 O 457 BOND = 961.4863 ANGLE = 28071.2413 DIHED = 1686.1436 VDWAALS = ************* EEL = -22338.6619 HBOND = 0.0000 1-4 VDW = ************* 1-4 EEL = 5974.0453 CONSTRAINT = 0.0000