------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 02/13/2007 at 19:01:49 [-O]verwriting output File Assignments: | MDIN: ./NSER.16.min1 | MDOUT: ./NSER.16.outm1 |INPCRD: ./NSER.16.xyz | PARM: NSER.16.tpp |RESTRT: ./NSER.16.rst1 | REFC: ./NSER.16.xyz | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: ./NSER.16.mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Minimization &cntrl imin=1, ntr=0, cut=6, ntpr=100, scee=1.2, drms=0.0001, maxcyc= 3000, ntmin=1, ncyc=1000, nsnb=25, dielc = 4.0, &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: getting new box info from bottom of inpcrd | peek_ewald_inpcrd: Box info found |Largest sphere to fit in unit cell has radius = 8.000 | New format PARM file being parsed. | Version = 1.000 Date = 02/13/07 Time = 18:38:26 NATOM = 13 NTYPES = 9 NBONH = 7 MBONA = 5 NTHETH = 15 MTHETA = 5 NPHIH = 21 MPHIA = 4 NHPARM = 0 NPARM = 0 NNB = 58 NRES = 1 NBONA = 5 NTHETA = 5 NPHIA = 4 NUMBND = 9 NUMANG = 14 NPTRA = 5 NATYP = 9 NPHB = 0 IFBOX = 1 NMXRS = 13 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 86632 | Hollerith 81 | Integer 42424 | Max Pairs 78 | Max Rstack 11618 | Max Istack 65 | Total 934 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- NSER 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 = 100, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 4.00000, cut = 6.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 3000, ncyc = 1000, ntmin = 1 dx0 = 0.01000, drms = 0.00010 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 16.000 Box Y = 16.000 Box Z = 16.000 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 16 NFFT2 = 16 NFFT3 = 16 Cutoff= 6.000 Tol =0.100E-04 Ewald Coefficient = 0.47291 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- NSER begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 Sum of charges from parm topology file = 0.50000000 Assuming uniform neutralizing plasma -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- Exceeding lastrst in get_stack lastrst = 11618 top_stk= 0 isize = 21281 request= 21281 Increase lastrst in the &cntrl namelist