------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 03/30/2009 at 11:18:46 File Assignments: | MDIN: /home/student/remya/dnaexer1/dna_fmd.in | MDOUT: /home/student/remya/dnaexer1/dnafmd.out |INPCRD: /home/student/remya/dnaexer1/dna_min55.rst | PARM: /home/student/remya/dnaexer1/dna_wat.prmtop |RESTRT: /home/student/remya/dnaexer1/dnafmd.rst | REFC: /home/student/remya/dnaexer1/dna_min55.rst | MDVEL: mdvel | MDEN: mden | MDCRD: /home/student/remya/dnaexer1/dnafmd.mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | Here is the input file: dna :10ps MD with res on DNA &cntrl imin = 0, irest = 0, ntx = 1, ntb = 1, cut = 10.0, ntr = 1, ntc = 2, ntf = 2, tempi = 100.0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0, nstlim = 5000, dt = 0.002 ntpr = 100, ntwx = 100, ntwr = 1000 / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: 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 = 24.756 | New format PARM file being parsed. | Version = 1.000 Date = 03/18/09 Time = 12:32:49 NATOM = 14545 NTYPES = 16 NBONH = 14029 MBONA = 550 NTHETH = 636 MTHETA = 844 NPHIH = 1354 MPHIA = 1480 NHPARM = 0 NPARM = 0 NNB = 22586 NRES = 4635 NBONA = 550 NTHETA = 844 NPHIA = 1480 NUMBND = 37 NUMANG = 73 NPTRA = 41 NATYP = 26 NPHB = 1 IFBOX = 2 NMXRS = 33 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 840288 | Hollerith 91907 | Integer 391395 | Max Pairs 8377920 | nblistReal 174540 | nblist Int 487552 | Total 44447 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- 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 = 5000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 71277 temp0 = 300.00000, tempi = 100.00000, 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 = 60.640 Box Y = 60.640 Box Z = 60.640 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 60 NFFT2 = 60 NFFT3 = 60 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES ----- READING GROUP 1; TITLE: GROUP 1 HAS HARMONIC CONSTRAINTS 0.00000 rfree: End of file on unit 5