------------------------------------------------------- Amber 7 SANDER Scripps/UCSF 2002 ------------------------------------------------------- | Mon Nov 22 12:08:02 2004 [-O]verwriting output File Assignments: | MDIN: /disk6/kepa/ambercal/1bencenoDM/1box/b1boxDM1.in | MDOUT: /disk6/kepa/ambercal/1bencenoDM/1box/b1boxDM1.out |INPCRD: /disk6/kepa/ambercal/1bencenoDM/1box/b1boxDM1.crd | PARM: /disk6/kepa/ambercal/1bencenoDM/1box/b1boxDM1.top |RESTRT: /disk6/kepa/ambercal/1bencenoDM/1box/b1boxDM1.rst | REFC: refc | MDVEL: /disk6/kepa/ambercal/1bencenoDM/1box/b1boxDM1.vel | MDEN: /disk6/kepa/ambercal/1bencenoDM/1box/b1boxDM1.erg | MDCRD: /disk6/kepa/ambercal/1bencenoDM/1box/b1boxDM1.trj |MDINFO: /disk6/kepa/ambercal/1bencenoDM/1box/b1boxDM1.inf |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: b1box &cntrl imin=0, nmropt=1, ntx=1, irest=0, ntrx=1, ntxo=1, ntpr=1000, ntwr=1000, iwrap=1, ntwx=1000, ntwv=1000, ntwe=1000, ioutfm=0, ntwprt=0, idecomp=0, ntf=3, ntb=1, igb=0, nsnb=25, ipol=0, gbsa=0, dielc=1.0, cut=12.0, intdiel=1.0, scnb=2.0, scee=1.2, nstlim=200000, nscm=1000, nrespa=1, t=0.0, dt=0.001, vlimit=20.0, ig=71277, ntt=1, vrand=0, temp0= 375.0, tempi=0.0, heat=0.0, dtemp=5.0, tautp =0.5, ntc=3, tol=0.00001 &end &wt type='TEMP0', istep1=0, istep2=50000, value1=0.0, value2=375.0, &end &wt type='TEMP0', istep1=50001, istep2=200000, value1=375.0, value2=375.0, &en &wt type='END' &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MEM_ALLOC getting new box info from bottom of inpcrd | peek_ewald_inpcrd: Box info found | New format PARM file being parsed. | Version = 1.000 Date = 11/05/04 Time = 01:26:19 NATOM = 3588 NTYPES = 2 NBONH = 1794 MBONA = 1794 NTHETH = 3588 MTHETA = 1794 NPHIH = 7176 MPHIA = 1794 NHPARM = 0 NPARM = 0 NNB = 15548 NRES = 299 NBONA = 1794 NTHETA = 1794 NPHIA = 1794 NUMBND = 2 NUMANG = 2 NPTRA = 2 NATYP = 2 NPHB = 0 IFBOX = 1 NMXRS = 12 IFCAP = 0 NEXTRA = 0 | Memory Use Allocated | Real 314278 | Hollerith 21829 | Integer 1086669 | Max Pairs 2812992 | Max Rstack 2000000 | Max Istack 2000000 | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- bB1 General flags: imin = 0, nmropt = 1 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 1000, ntrx = 1, ntwr = 1000 iwrap = 1, ntwx = 1000, ntwv = 1000, ntwe = 1000 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 3, ntb = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0 dielc = 1.00000, cut = 12.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 200000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 20.00000 Temperature regulation: ig = 71277, ntt = 1, vrand = 0 temp0 = 375.00000, tempi = 0.00000, heat = 0.00000 dtemp = 5.00000, tautp = 0.50000 SHAKE: ntc = 3, jfastw = 0 tol = 0.00001 NMR refinement options: iscale = 0, noeskp = 1, ipnlty = 1, mxcub = 1 scalm = 100.00000, pencut = 0.10000, tausw = 0.10000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, frc_int = 0, netfrc = 1 Box X = 100.000 Box Y = 100.000 Box Z = 100.000 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 100 NFFT2 = 100 NFFT3 = 100 Cutoff= 12.000 Tol =0.100E-04 Ewald Coefficient = 0.22664 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- bB1 begin time read from input coords = 0.000 ps Begin reading energy term weight changes/NMR restraints WEIGHT CHANGES: TEMP0 0 50000 0.000000 375.000000 0 0 TEMP0 50001 200000 375.000000 375.000000 0 0 RESTRAINTS: ** No restraint defined ** Done reading weight changes/NMR restraints Number of triangulated 3-point waters found: 0 Sum of charges from parm topology file = 0.00000000 Forcing neutrality... -------------------------------------------------------------------------------- 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 = 0.3242E-14 at 2.436720 | CHECK d/dx switch(x): max rel err = 0.7977E-11 at 2.712040 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 1013859 | TOTAL SIZE OF NONBOND LIST = 1013859 Exceeding lastrst lastrst = 2000000 top_stk= 1050602 isize = 1060904 request= 2111506 Increase lastrst in the &cntrl namelist