------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 08/28/2007 at 17:56:41 [-O]verwriting output File Assignments: | MDIN: heat1.in | MDOUT: heat1.out |INPCRD: min_classical.rst | PARM: EQE.prmtop |RESTRT: heat1.rst | REFC: min_classical.rst | MDVEL: mdvel | MDEN: mden | MDCRD: heat1.mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Stage 1 heating of solute/solvent &cntrl imin=0, irest=0, ntx=1, ntb=1, ntr=1, ntc=2, ntf=2, tempi=0.0, temp0=50.0, ntt=3, gamma_ln=1.0, cut=10.0, nstlim=10000, dt=0.0015, ntpr=100, ntwx=100, ntwr=1000 / Keep EQE fixed with weak restraint 10.0 -------------------------------------------------------------------------------- 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 = 20.977 | New format PARM file being parsed. | Version = 1.000 Date = 08/27/07 Time = 16:26:28 NATOM = 7688 NTYPES = 11 NBONH = 5104 MBONA = 1324 NTHETH = 8949 MTHETA = 86 NPHIH = 3927 MPHIA = 149 NHPARM = 0 NPARM = 0 NNB = 20762 NRES = 1266 NBONA = 1324 NTHETA = 86 NPHIA = 149 NUMBND = 25 NUMANG = 46 NPTRA = 22 NATYP = 16 NPHB = 0 IFBOX = 1 NMXRS = 98 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 502779 | Hollerith 47396 | Integer 321849 | Max Pairs 1107072 | nblistReal 92256 | nblist Int 304422 | Total 11604 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- EQE General flags: imin = 0, 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 = 1000 iwrap = 0, ntwx = 100, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 10.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 1 Molecular dynamics: nstlim = 10000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00150, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 71277 temp0 = 50.00000, tempi = 0.00000, gamma_ln= 1.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 47.788 Box Y = 57.976 Box Z = 41.954 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 48 NFFT2 = 60 NFFT3 = 45 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES EQE ----- READING GROUP 1; TITLE: Keep EQE fixed with weak restraint GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000 rfree: End of file on unit 5