possible FAILURE: check umbrella.ncdump.dif /home/jacky/amber16/test/nfe/abmd_FLOODING 0a1,25 > netcdf ncdump { > dimensions: > row-major = 41 ; > variables: > double coeffs(row-major) ; > coeffs:C_format = "%14.10f" ; > // global attributes: > :nextents = 1 ; > :extents = 41 ; > :periodicity = 0 ; > :origin = 0. ; > :spacing = 0.25 ; > data: > coeffs = 0., 0., 0., 0., > 0., 0., 0., 0., > 0., 0., 0., 0., > 0., 0., 0., 0., > 0., 0., 0., 0., > 0., 0., 0., 0.0000297317, > 0.0595638029, 0.1163618241, 0.0716093406, 0.0007783546, > 0., 0., 0., 0., > 0., 0., 0., 0., > 0., 0., 0., 0., > 0. ; > } --------------------------------------- possible FAILURE: check wt_umbrella.ncdump.dif /home/jacky/amber16/test/nfe/abmd_FLOODING 0a1,25 > netcdf ncdump { > dimensions: > row-major = 41 ; > variables: > double coeffs(row-major) ; > coeffs:C_format = "%14.10f" ; > // global attributes: > :nextents = 1 ; > :extents = 41 ; > :periodicity = 0 ; > :origin = 0. ; > :spacing = 0.25 ; > data: > coeffs = 0., 0., 0., 0., > 0., 0., 0., 0., > 0., 0., 0., 0., > 0., 0., 0., 0., > 0., 0., 0., 0., > 0., 0., 0., 0.0000306236, > 0.0613507170, 0.1198526788, 0.0737576208, 0.0008017052, > 0., 0., 0., 0., > 0., 0., 0., 0., > 0., 0., 0., 0., > 0. ; > } --------------------------------------- possible FAILURE: check mdout.dif /home/jacky/amber16/test/nfe/abmd_UMBRELLA 84,225c84 < NFE : () () () () () () () () () () A. B. M. D. () () () () () () () () () < NFE : < NFE : mode = UMBRELLA < NFE : < NFE : CV #1 < NFE : type = 'MULTI_RMSD' < NFE : <> group <> #1: < NFE : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], < NFE : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], < NFE : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], < NFE : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], < NFE : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], < NFE : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) < NFE : reference coordinates : < NFE : 1 : -0.29, 4.03, -17.15 < NFE : 5 : 0.47, 4.46, -16.54 < NFE : 8 : 1.93, 4.40, -16.85 < NFE : 10 : 2.78, 4.75, -16.00 < NFE : 12 : 4.24, 4.79, -16.12 < NFE : 29 : 4.93, 4.19, -14.90 < NFE : 31 : 6.13, 3.68, -15.06 < NFE : 33 : 6.94, 3.05, -14.02 < NFE : 41 : 8.38, 3.58, -14.03 < NFE : 43 : 8.73, 4.54, -13.17 < NFE : 53 : 10.07, 5.08, -13.08 < NFE : 55 : 11.16, 4.09, -12.71 < NFE : 57 : 10.86, 2.98, -12.09 < NFE : 59 : 11.82, 1.94, -11.73 < NFE : 70 : 12.35, 1.16, -12.92 < NFE : 72 : 11.67, 1.15, -14.03 < NFE : 74 : 12.09, 0.51, -15.29 < NFE : 84 : 12.13, 1.46, -16.47 < NFE : 86 : 11.48, 2.61, -16.39 < NFE : 88 : 11.36, 3.58, -17.46 < NFE : 91 : 10.38, 3.19, -18.54 < NFE : 93 : 9.30, 2.52, -18.22 < NFE : 95 : 8.35, 1.93, -19.17 < NFE : 105 : 6.91, 2.35, -18.92 < NFE : 107 : 6.06, 2.25, -19.92 < NFE : 109 : 4.66, 2.61, -19.91 < NFE : 129 : 3.76, 1.41, -19.92 < NFE : 131 : 2.69, 1.45, -19.46 < NFE : 133 : 1.69, 0.44, -19.40 < NFE : 136 : 0.61, 0.77, -18.87 < NFE : < NFE : monitor_file = monitor.txt < NFE : monitor_freq = 1 (0.002 ps) < NFE : umbrella_file = umbrella.nc (loaded) < NFE : < NFE : umbrella discretization (unchanged) : < NFE : CV #1 not periodic, 41 points, min/max = 0./10.00000 < NFE : < NFE : () () () () () () () () () () () () () () () () () () () () () () () () < NSTEP = 5 TIME(PS) = 0.01 TEMP(K) = 302.6 PRESS = 0. < Etot = -8321.484 EKtot = 1914.181 EPtot = -10235.665 < BOND = 19.073 ANGLE = 63.592 DIHED = 72.696 < 1-4 NB = 31.932 1-4 EEL = 541.000 VDWAALS = 1297.273 < EELEC = -12261.233 EHBOND = 0. RESTRAINT = 0. < Ewald error estimate: 0.563E-3 < ------------------------------------------------------------------------------ < NSTEP = 10 TIME(PS) = 0.02 TEMP(K) = 303.1 PRESS = 0. < Etot = -8329.331 EKtot = 1917.162 EPtot = -10246.494 < BOND = 25.274 ANGLE = 68.106 DIHED = 73.104 < 1-4 NB = 34.018 1-4 EEL = 541.644 VDWAALS = 1326.260 < EELEC = -12314.902 EHBOND = 0. RESTRAINT = 0. < Ewald error estimate: 0.291E-3 < ------------------------------------------------------------------------------ < NSTEP = 15 TIME(PS) = 0.03 TEMP(K) = 297.2 PRESS = 0. < Etot = -8320.077 EKtot = 1879.654 EPtot = -10199.731 < BOND = 25.730 ANGLE = 67.703 DIHED = 76.286 < 1-4 NB = 31.494 1-4 EEL = 535.046 VDWAALS = 1359.517 < EELEC = -12295.511 EHBOND = 0. RESTRAINT = 0. < Ewald error estimate: 0.142E-3 < ------------------------------------------------------------------------------ < NSTEP = 20 TIME(PS) = 0.04 TEMP(K) = 299.1 PRESS = 0. < Etot = -8311.959 EKtot = 1892.032 EPtot = -10203.991 < BOND = 32.830 ANGLE = 68.244 DIHED = 72.898 < 1-4 NB = 28.390 1-4 EEL = 536.412 VDWAALS = 1387.067 < EELEC = -12329.835 EHBOND = 0. RESTRAINT = 0. < Ewald error estimate: 0.263E-4 < ------------------------------------------------------------------------------ < NSTEP = 25 TIME(PS) = 0.05 TEMP(K) = 301.8 PRESS = 0. < Etot = -8313.587 EKtot = 1908.682 EPtot = -10222.270 < BOND = 35.445 ANGLE = 70.843 DIHED = 73.476 < 1-4 NB = 28.888 1-4 EEL = 538.884 VDWAALS = 1406.839 < EELEC = -12376.648 EHBOND = 0. RESTRAINT = 0. < Ewald error estimate: 0.306E-4 < ------------------------------------------------------------------------------ < NSTEP = 30 TIME(PS) = 0.06 TEMP(K) = 307.8 PRESS = 0. < Etot = -8308.139 EKtot = 1947.161 EPtot = -10255.300 < BOND = 32.860 ANGLE = 64.449 DIHED = 74.428 < 1-4 NB = 30.204 1-4 EEL = 534.520 VDWAALS = 1408.103 < EELEC = -12399.866 EHBOND = 0. RESTRAINT = 0. < Ewald error estimate: 0.744E-4 < ------------------------------------------------------------------------------ < NSTEP = 35 TIME(PS) = 0.07 TEMP(K) = 296.0 PRESS = 0. < Etot = -8312.354 EKtot = 1871.985 EPtot = -10184.339 < BOND = 23.747 ANGLE = 70.924 DIHED = 73.514 < 1-4 NB = 30.145 1-4 EEL = 531.150 VDWAALS = 1412.156 < EELEC = -12325.978 EHBOND = 0. RESTRAINT = 0. < Ewald error estimate: 0.716E-4 < ------------------------------------------------------------------------------ < NSTEP = 40 TIME(PS) = 0.08 TEMP(K) = 300.0 PRESS = 0. < Etot = -8316.332 EKtot = 1897.755 EPtot = -10214.088 < BOND = 27.618 ANGLE = 63.521 DIHED = 74.691 < 1-4 NB = 34.553 1-4 EEL = 531.049 VDWAALS = 1411.041 < EELEC = -12356.563 EHBOND = 0. RESTRAINT = 0. < Ewald error estimate: 0.267E-4 < ------------------------------------------------------------------------------ < NSTEP = 45 TIME(PS) = 0.09 TEMP(K) = 298.9 PRESS = 0. < Etot = -8320.693 EKtot = 1890.608 EPtot = -10211.301 < BOND = 29.075 ANGLE = 59.154 DIHED = 74.590 < 1-4 NB = 35.567 1-4 EEL = 533.225 VDWAALS = 1407.883 < EELEC = -12350.799 EHBOND = 0. RESTRAINT = 0. < Ewald error estimate: 0.156E-3 < ------------------------------------------------------------------------------ < NSTEP = 50 TIME(PS) = 0.10 TEMP(K) = 305.2 PRESS = 0. < Etot = -8323.456 EKtot = 1930.658 EPtot = -10254.114 < BOND = 22.640 ANGLE = 69.817 DIHED = 71.623 < 1-4 NB = 35.126 1-4 EEL = 535.016 VDWAALS = 1393.391 < EELEC = -12381.729 EHBOND = 0. RESTRAINT = 0. < Ewald error estimate: 0.103E-4 < ------------------------------------------------------------------------------ < A V E R A G E S O V E R 10 S T E P S < NSTEP = 50 TIME(PS) = 0.10 TEMP(K) = 301.2 PRESS = 0. < Etot = -8317.741 EKtot = 1904.988 EPtot = -10222.729 < BOND = 27.429 ANGLE = 66.635 DIHED = 73.731 < 1-4 NB = 32.032 1-4 EEL = 535.794 VDWAALS = 1380.953 < EELEC = -12339.306 EHBOND = 0. RESTRAINT = 0. < Ewald error estimate: 0.139E-3 < ------------------------------------------------------------------------------ < R M S F L U C T U A T I O N S < NSTEP = 50 TIME(PS) = 0.10 TEMP(K) = 3.4 PRESS = 0. < Etot = 6.075 EKtot = 22.004 EPtot = 23.102 < BOND = 4.894 ANGLE = 3.630 DIHED = 1.240 < 1-4 NB = 2.504 1-4 EEL = 3.531 VDWAALS = 38.283 < EELEC = 40.209 EHBOND = 0. RESTRAINT = 0. < Ewald error estimate: 0.163E-3 < ------------------------------------------------------------------------------ < -------------------------------------------------------------------------------- < 5. TIMINGS < -------------------------------------------------------------------------------- --- > ** NFError ** : umbrella_load(filename='umbrella.nc') : NetCDF: Unknown file format ---------------------------------------