------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 03/02/2008 at 10:42:11 [-O]verwriting output File Assignments: | MDIN: md.in | MDOUT: nexil8_md_ini.out |INPCRD: nexil8_even_min.rst | PARM: nexil8_even.top |RESTRT: nexil8_even_md_ini.rst | REFC: nexil8_even.crd | MDVEL: mdvel | MDEN: mden | MDCRD: nexil8_even_md_ini.mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: &cntrl timlim = 999999., nmropt = 0, imin=0, ntx = 1, irest = 0, ntrx = 1, ntxo = 1, ntpr = 100, ntwx = 100, ntwv = 0, ntwe = 0, ioutfm = 0, ntwr = 50000, ntwprt = 0, ntf = 2, ntb = 0, igb = 2, gbsa =1, surften=0.005, dielc = 1.0, cut = 16.0, nsnb = 10, scnb = 2.0, scee = 1.2, nstlim = 100000, nscm = 2500, iwrap = 0, t = 0.0, dt = 0.002, temp0 = 300.0, tempi = 200.0, tautp=0.5, ig = 71227, heat = 0.0, ntt = 3, gamma_ln=2.0, ntc = 2, tol = 0.00001, jfastw = 0, ibelly=0, ntr=0, &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- Warning: heat has been retired. Check the Retired Namelist Variables Appendix in the manual. Warning: timlim has been retired. Check the Retired Namelist Variables Appendix in the manual. | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 03/01/08 Time = 23:21:22 NATOM = 4821 NTYPES = 12 NBONH = 1974 MBONA = 2902 NTHETH = 4806 MTHETA = 3991 NPHIH = 11048 MPHIA = 6499 NHPARM = 0 NPARM = 0 NNB = 26771 NRES = 131 NBONA = 2902 NTHETA = 3991 NPHIA = 6499 NUMBND = 27 NUMANG = 69 NPTRA = 37 NATYP = 16 NPHB = 0 IFBOX = 0 NMXRS = 141 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) | Memory Use Allocated | Real 275209 | Hollerith 29059 | Integer 462305 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 4069 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- NML 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 = 50000 iwrap = 0, ntwx = 100, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 0, igb = 2, nsnb = 10 ipol = 0, gbsa = 1, iesp = 0 dielc = 1.00000, cut = 16.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 0.80000 gbbeta = 0.00000, gbgamma = 2.90912, surften = 0.00500 rdt = 0.00000, rgbmax = 25.00000 alpb = 0 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 100000, nscm = 2500, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 71227 temp0 = 300.00000, tempi = 200.00000, gamma_ln= 2.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES --------------------------------------------------------------------------------