1# 2# sialic acid 3# 4 5System.CurrrentDirectory ./ # default=./ 6System.Name SialicAcid 7level.of.stdout 1 # default=1 (1-3) 8level.of.fileout 1 # default=1 (1-3) 9 10# 11# Definition of Atomic Species 12# 13 14Species.Number 4 15<Definition.of.Atomic.Species 16 H H7.0-s2 H_PBE13 17 C C7.0-s2p2d1 C_PBE13 18 N N7.0-s2p2d1 N_PBE13 19 O O7.0-s2p2d1 O_PBE13 20Definition.of.Atomic.Species> 21 22# 23# Atoms 24# 25 26Atoms.Number 40 27Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU 28<Atoms.SpeciesAndCoordinates # Unit=Ang. 29 1 C 2.582389 0.082263 0.275981 2.0 2.0 30 2 C 2.373302 -1.138641 1.194045 2.0 2.0 31 3 C 1.025279 -1.046303 1.915805 2.0 2.0 32 4 O 1.494760 0.417412 -0.551026 3.0 3.0 33 5 O 2.737365 1.290409 0.959881 3.0 3.0 34 6 C 3.786642 -0.218196 -0.669598 2.0 2.0 35 7 C -0.094548 -0.880994 0.852978 2.0 2.0 36 8 O 0.818810 -2.142299 2.769607 3.0 3.0 37 9 C 0.189860 0.406427 0.032303 2.0 2.0 38 10 O 3.643031 -0.765984 -1.887826 3.0 3.0 39 11 N -1.439593 -0.763227 1.473170 2.5 2.5 40 12 C -0.794830 0.555420 -1.164775 2.0 2.0 41 13 C -2.201474 -1.933622 1.785979 2.0 2.0 42 14 C -0.699037 1.970172 -1.816905 2.0 2.0 43 15 O -0.492165 -0.473838 -2.086758 3.0 3.0 44 16 C -3.380212 -1.734942 2.703342 2.0 2.0 45 17 C -1.692264 2.084875 -3.001286 2.0 2.0 46 18 O -1.043670 2.903447 -0.812168 3.0 3.0 47 19 O -1.330304 3.229879 -3.734910 3.0 3.0 48 20 H 2.425174 -2.068894 0.591604 0.5 0.5 49 21 H 3.200545 -1.206435 1.928208 0.5 0.5 50 22 H 1.026448 -0.193694 2.636486 0.5 0.5 51 23 H 3.581516 1.287328 1.392610 0.5 0.5 52 24 O 4.952256 -0.033514 -0.388556 3.0 3.0 53 25 H -0.102022 -1.766810 0.166650 0.5 0.5 54 26 H 0.735183 -2.921643 2.231726 0.5 0.5 55 27 H 0.107549 1.303998 0.694823 0.5 0.5 56 28 H 2.725125 -0.850757 -2.119188 0.5 0.5 57 29 H -1.471475 -0.065661 2.186538 0.5 0.5 58 30 H -1.836523 0.400014 -0.786384 0.5 0.5 59 31 O -1.917639 -2.999691 1.261455 3.0 3.0 60 32 H 0.345774 2.154635 -2.170503 0.5 0.5 61 33 H -0.997689 -0.290669 -2.871991 0.5 0.5 62 34 H -4.034390 -0.927209 2.348403 0.5 0.5 63 35 H -3.989613 -2.645567 2.777278 0.5 0.5 64 36 H -3.048059 -1.477466 3.718235 0.5 0.5 65 37 H -1.627818 1.184534 -3.650635 0.5 0.5 66 38 H -2.737481 2.157517 -2.640910 0.5 0.5 67 39 H -0.814953 3.755808 -1.157336 0.5 0.5 68 40 H -2.005246 3.361919 -4.386353 0.5 0.5 69Atoms.SpeciesAndCoordinates> 70Atoms.UnitVectors.Unit Ang # Ang|AU 71<Atoms.UnitVectors 72 16.0 0.0 0.0 73 0.0 14.0 0.0 74 0.0 0.0 15.0 75Atoms.UnitVectors> 76 77# 78# SCF or Electronic System 79# 80 81scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW 82scf.SpinPolarization off # On|Off 83scf.ElectronicTemperature 900.0 # default=300 (K) 84scf.energycutoff 150.0 # default=150 (Ry) 85scf.maxIter 100 # default=40 86scf.EigenvalueSolver cluster # Recursion|Cluster|Band 87scf.Kgrid 1 1 1 # means 4x4x4 88scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay 89scf.Init.Mixing.Weight 0.100 # default=0.30 90scf.Min.Mixing.Weight 0.001 # default=0.001 91scf.Max.Mixing.Weight 0.600 # default=0.40 92scf.Mixing.History 15 # default=5 93scf.Mixing.StartPulay 9 # default=6 94scf.criterion 1.0e-10 # default=1.0e-6 (Hartree) 95 96# 97# MD or Geometry Optimization 98# 99 100MD.Type nomd # Nomd|Opt|NVE|NVT_VS|NVT_NH 101MD.maxIter 1 # default=1 102MD.TimeStep 1.0 # default=0.5 (fs) 103MD.Opt.criterion 1.0e-4 # default=1.0e-4 (Hartree/bohr) 104 105