possible FAILURE:  check gcg.dip.o.dif
/home/tolsan83/amber10/test/rdc
352c352
<       196 H5'1 DA     7      0.14      0.62      0.96
---
>       196 H5'1 DA     7      0.14      0.63      0.96
377c377
<       512 H5'1 DA    17      0.13      0.62      0.98
---
>       512 H5'1 DA    17      0.13      0.63      0.98
---------------------------------------
possible FAILURE:  check stem.dip.o.dif
/home/tolsan83/amber10/test/pcsa
---------------------------------------
possible FAILURE:  check output_addles.dif
/home/tolsan83/amber10/test/LES
---------------------------------------
possible FAILURE:  check LES.prmtop.dif
/home/tolsan83/amber10/test/LES
---------------------------------------
possible FAILURE:  check addles.out.dif
/home/tolsan83/amber10/test/PIMD/part_pimd_water
---------------------------------------
possible FAILURE:  check addles.out.dif
/home/tolsan83/amber10/test/ti_mass/pent_LES_PIMD
---------------------------------------
possible FAILURE:  check amoeba_jac.mdout.dif
/home/tolsan83/amber10/test/amoeba_jac
---------------------------------------
possible FAILURE:  check mdout.dif
/home/tolsan83/amber10/test/ncsu/abmd_ANALYSIS
103,233c103
<  NCSU : () () () () () () () () () ()   A. B. M. D.  () () () () () () () () ()
<  NCSU :
<  NCSU : mode = ANALYSIS
<  NCSU :
<  NCSU : CV #1
<  NCSU :   type = 'MULTI_RMSD'
<  NCSU : <> group <> #1:
<  NCSU : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA],
<  NCSU :    29 [C], 31 [N], 33 [CA], 41 [C], 43 [N],
<  NCSU :    53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C],
<  NCSU :    72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA],
<  NCSU :    91 [C], 93 [N], 95 [CA], 105 [C], 107 [N],
<  NCSU :    109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C])
<  NCSU : reference coordinates :
<  NCSU :        1 :   -0.29,    4.03,  -17.15
<  NCSU :        5 :    0.47,    4.46,  -16.54
<  NCSU :        8 :    1.93,    4.40,  -16.85
<  NCSU :       10 :    2.78,    4.75,  -16.00
<  NCSU :       12 :    4.24,    4.79,  -16.12
<  NCSU :       29 :    4.93,    4.19,  -14.90
<  NCSU :       31 :    6.13,    3.68,  -15.06
<  NCSU :       33 :    6.94,    3.05,  -14.02
<  NCSU :       41 :    8.38,    3.58,  -14.03
<  NCSU :       43 :    8.73,    4.54,  -13.17
<  NCSU :       53 :   10.07,    5.08,  -13.08
<  NCSU :       55 :   11.16,    4.09,  -12.71
<  NCSU :       57 :   10.86,    2.98,  -12.09
<  NCSU :       59 :   11.82,    1.94,  -11.73
<  NCSU :       70 :   12.35,    1.16,  -12.92
<  NCSU :       72 :   11.67,    1.15,  -14.03
<  NCSU :       74 :   12.09,    0.51,  -15.29
<  NCSU :       84 :   12.13,    1.46,  -16.47
<  NCSU :       86 :   11.48,    2.61,  -16.39
<  NCSU :       88 :   11.36,    3.58,  -17.46
<  NCSU :       91 :   10.38,    3.19,  -18.54
<  NCSU :       93 :    9.30,    2.52,  -18.22
<  NCSU :       95 :    8.35,    1.93,  -19.17
<  NCSU :      105 :    6.91,    2.35,  -18.92
<  NCSU :      107 :    6.06,    2.25,  -19.92
<  NCSU :      109 :    4.66,    2.61,  -19.91
<  NCSU :      129 :    3.76,    1.41,  -19.92
<  NCSU :      131 :    2.69,    1.45,  -19.46
<  NCSU :      133 :    1.69,    0.44,  -19.40
<  NCSU :      136 :    0.61,    0.77,  -18.87
<  NCSU :
<  NCSU : monitor_file = monitor.txt
<  NCSU : monitor_freq = 1 (0.002 ps)
<  NCSU :
<  NCSU : () () () () () () () () () () () () () () () () () () () () () () () ()
<  ---------------------------------------------------
<  APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
<  using   5000. points per unit in tabled values
<  TESTING RELATIVE ERROR over r ranging from 0. to cutoff
<  ---------------------------------------------------
<  NSTEP =        5   TIME(PS) =       0.01  TEMP(K) =   302.6  PRESS =     0.
<  Etot   =     -8321.483  EKtot   =      1914.182  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.
<  ------------------------------------------------------------------------------
<  NSTEP =       10   TIME(PS) =       0.02  TEMP(K) =   303.1  PRESS =     0.
<  Etot   =     -8329.330  EKtot   =      1917.163  EPtot      =    -10246.494
<  BOND   =        25.274  ANGLE   =        68.106  DIHED      =        73.104
<  1-4 NB =        34.017  1-4 EEL =       541.643  VDWAALS    =      1326.260
<  EELEC  =    -12314.902  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       15   TIME(PS) =       0.03  TEMP(K) =   297.2  PRESS =     0.
<  Etot   =     -8320.076  EKtot   =      1879.655  EPtot      =    -10199.731
<  BOND   =        25.731  ANGLE   =        67.704  DIHED      =        76.286
<  1-4 NB =        31.494  1-4 EEL =       535.045  VDWAALS    =      1359.517
<  EELEC  =    -12295.510  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       20   TIME(PS) =       0.04  TEMP(K) =   299.1  PRESS =     0.
<  Etot   =     -8311.958  EKtot   =      1892.032  EPtot      =    -10203.990
<  BOND   =        32.830  ANGLE   =        68.244  DIHED      =        72.898
<  1-4 NB =        28.390  1-4 EEL =       536.411  VDWAALS    =      1387.068
<  EELEC  =    -12329.834  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       25   TIME(PS) =       0.05  TEMP(K) =   301.8  PRESS =     0.
<  Etot   =     -8313.586  EKtot   =      1908.683  EPtot      =    -10222.269
<  BOND   =        35.446  ANGLE   =        70.843  DIHED      =        73.476
<  1-4 NB =        28.888  1-4 EEL =       538.883  VDWAALS    =      1406.839
<  EELEC  =    -12376.647  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       30   TIME(PS) =       0.06  TEMP(K) =   307.8  PRESS =     0.
<  Etot   =     -8308.138  EKtot   =      1947.161  EPtot      =    -10255.300
<  BOND   =        32.860  ANGLE   =        64.449  DIHED      =        74.428
<  1-4 NB =        30.204  1-4 EEL =       534.519  VDWAALS    =      1408.103
<  EELEC  =    -12399.866  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  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   =        70.925  DIHED      =        73.514
<  1-4 NB =        30.145  1-4 EEL =       531.149  VDWAALS    =      1412.155
<  EELEC  =    -12325.978  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       40   TIME(PS) =       0.08  TEMP(K) =   300.0  PRESS =     0.
<  Etot   =     -8316.331  EKtot   =      1897.756  EPtot      =    -10214.087
<  BOND   =        27.618  ANGLE   =        63.521  DIHED      =        74.691
<  1-4 NB =        34.553  1-4 EEL =       531.049  VDWAALS    =      1411.040
<  EELEC  =    -12356.562  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       45   TIME(PS) =       0.09  TEMP(K) =   298.9  PRESS =     0.
<  Etot   =     -8320.692  EKtot   =      1890.608  EPtot      =    -10211.301
<  BOND   =        29.075  ANGLE   =        59.154  DIHED      =        74.590
<  1-4 NB =        35.567  1-4 EEL =       533.226  VDWAALS    =      1407.882
<  EELEC  =    -12350.799  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       50   TIME(PS) =       0.10  TEMP(K) =   305.2  PRESS =     0.
<  Etot   =     -8323.455  EKtot   =      1930.658  EPtot      =    -10254.114
<  BOND   =        22.640  ANGLE   =        69.817  DIHED      =        71.623
<  1-4 NB =        35.126  1-4 EEL =       535.017  VDWAALS    =      1393.391
<  EELEC  =    -12381.729  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<       A V E R A G E S   O V E R      50 S T E P S
<  NSTEP =       50   TIME(PS) =       0.10  TEMP(K) =   300.6  PRESS =     0.
<  Etot   =     -8317.366  EKtot   =      1901.322  EPtot      =    -10218.688
<  BOND   =        28.949  ANGLE   =        67.572  DIHED      =        73.819
<  1-4 NB =        31.971  1-4 EEL =       536.040  VDWAALS    =      1376.209
<  EELEC  =    -12333.251  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<       R M S  F L U C T U A T I O N S
<  NSTEP =       50   TIME(PS) =       0.10  TEMP(K) =     3.2  PRESS =     0.
<  Etot   =         6.900  EKtot   =        20.558  EPtot      =        20.606
<  BOND   =         4.608  ANGLE   =         4.103  DIHED      =         1.950
<  1-4 NB =         2.404  1-4 EEL =         3.752  VDWAALS    =        43.558
<  EELEC  =        42.131  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---
>  ** NCSU-Error ** : expected list value for key 'i', got '<EMPTY>' instead
---------------------------------------
possible FAILURE:  check monitor.txt.dif
/home/tolsan83/amber10/test/ncsu/abmd_ANALYSIS
1,53d0
< #
< # MD time (ps), CV #1
< #
<       0.     6.231568206
<       0.002     6.234804122
<       0.004     6.238046031
<       0.006     6.241400757
<       0.008     6.244754840
<       0.010     6.248257451
<       0.012     6.251783590
<       0.014     6.255299775
<       0.016     6.258596084
<       0.018     6.261494271
<       0.020     6.263587850
<       0.022     6.264792348
<       0.024     6.265061347
<       0.026     6.264482505
<       0.028     6.263601079
<       0.030     6.262856231
<       0.032     6.262420264
<       0.034     6.262560684
<       0.036     6.263103491
<       0.038     6.263728381
<       0.040     6.264545950
<       0.042     6.265497672
<       0.044     6.266693314
<       0.046     6.268208194
<       0.048     6.269950107
<       0.050     6.271994738
<       0.052     6.274069401
<       0.054     6.276230797
<       0.056     6.278056208
<       0.058     6.279344594
<       0.060     6.279950899
<       0.062     6.279870078
<       0.064     6.279290529
<       0.066     6.278354806
<       0.068     6.277440060
<       0.070     6.276583455
<       0.072     6.276113972
<       0.074     6.276134286
<       0.076     6.276326126
<       0.078     6.276801627
<       0.080     6.277535949
<       0.082     6.278230776
<       0.084     6.278645030
<       0.086     6.278689405
<       0.088     6.278437879
<       0.090     6.277758290
<       0.092     6.276779362
<       0.094     6.275507273
<       0.096     6.274326390
<       0.098     6.273388512
---------------------------------------
possible FAILURE:  check mdout.dif
/home/tolsan83/amber10/test/ncsu/abmd_FLOODING
106,242c106
<  NCSU : () () () () () () () () () ()   A. B. M. D.  () () () () () () () () ()
<  NCSU :
<  NCSU : mode = FLOODING
<  NCSU :
<  NCSU : CV #1
<  NCSU :   type = 'MULTI_RMSD'
<  NCSU : <> group <> #1:
<  NCSU : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA],
<  NCSU :    29 [C], 31 [N], 33 [CA], 41 [C], 43 [N],
<  NCSU :    53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C],
<  NCSU :    72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA],
<  NCSU :    91 [C], 93 [N], 95 [CA], 105 [C], 107 [N],
<  NCSU :    109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C])
<  NCSU : reference coordinates :
<  NCSU :        1 :   -0.29,    4.03,  -17.15
<  NCSU :        5 :    0.47,    4.46,  -16.54
<  NCSU :        8 :    1.93,    4.40,  -16.85
<  NCSU :       10 :    2.78,    4.75,  -16.00
<  NCSU :       12 :    4.24,    4.79,  -16.12
<  NCSU :       29 :    4.93,    4.19,  -14.90
<  NCSU :       31 :    6.13,    3.68,  -15.06
<  NCSU :       33 :    6.94,    3.05,  -14.02
<  NCSU :       41 :    8.38,    3.58,  -14.03
<  NCSU :       43 :    8.73,    4.54,  -13.17
<  NCSU :       53 :   10.07,    5.08,  -13.08
<  NCSU :       55 :   11.16,    4.09,  -12.71
<  NCSU :       57 :   10.86,    2.98,  -12.09
<  NCSU :       59 :   11.82,    1.94,  -11.73
<  NCSU :       70 :   12.35,    1.16,  -12.92
<  NCSU :       72 :   11.67,    1.15,  -14.03
<  NCSU :       74 :   12.09,    0.51,  -15.29
<  NCSU :       84 :   12.13,    1.46,  -16.47
<  NCSU :       86 :   11.48,    2.61,  -16.39
<  NCSU :       88 :   11.36,    3.58,  -17.46
<  NCSU :       91 :   10.38,    3.19,  -18.54
<  NCSU :       93 :    9.30,    2.52,  -18.22
<  NCSU :       95 :    8.35,    1.93,  -19.17
<  NCSU :      105 :    6.91,    2.35,  -18.92
<  NCSU :      107 :    6.06,    2.25,  -19.92
<  NCSU :      109 :    4.66,    2.61,  -19.91
<  NCSU :      129 :    3.76,    1.41,  -19.92
<  NCSU :      131 :    2.69,    1.45,  -19.46
<  NCSU :      133 :    1.69,    0.44,  -19.40
<  NCSU :      136 :    0.61,    0.77,  -18.87
<  NCSU :
<  NCSU : monitor_file = monitor.txt
<  NCSU : monitor_freq = 1 (0.002 ps)
<  NCSU : umbrella_file = umbrella.nc (not found)
<  NCSU :
<  NCSU : umbrella discretization (new) :
<  NCSU : CV #1 not periodic, 41 points, min/max = 0./10.00000
<  NCSU :
<  NCSU : flooding timescale = 1.00 ps
<  NCSU :
<  NCSU : () () () () () () () () () () () () () () () () () () () () () () () ()
<  ---------------------------------------------------
<  APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
<  using   5000. points per unit in tabled values
<  TESTING RELATIVE ERROR over r ranging from 0. to cutoff
<  ---------------------------------------------------
<  NSTEP =        5   TIME(PS) =       0.01  TEMP(K) =   302.6  PRESS =     0.
<  Etot   =     -8321.483  EKtot   =      1914.182  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.
<  ------------------------------------------------------------------------------
<  NSTEP =       10   TIME(PS) =       0.02  TEMP(K) =   303.1  PRESS =     0.
<  Etot   =     -8329.330  EKtot   =      1917.163  EPtot      =    -10246.494
<  BOND   =        25.274  ANGLE   =        68.106  DIHED      =        73.104
<  1-4 NB =        34.017  1-4 EEL =       541.643  VDWAALS    =      1326.260
<  EELEC  =    -12314.902  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       15   TIME(PS) =       0.03  TEMP(K) =   297.2  PRESS =     0.
<  Etot   =     -8320.075  EKtot   =      1879.655  EPtot      =    -10199.731
<  BOND   =        25.731  ANGLE   =        67.704  DIHED      =        76.286
<  1-4 NB =        31.494  1-4 EEL =       535.045  VDWAALS    =      1359.517
<  EELEC  =    -12295.510  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       20   TIME(PS) =       0.04  TEMP(K) =   299.1  PRESS =     0.
<  Etot   =     -8311.958  EKtot   =      1892.033  EPtot      =    -10203.991
<  BOND   =        32.830  ANGLE   =        68.244  DIHED      =        72.898
<  1-4 NB =        28.390  1-4 EEL =       536.411  VDWAALS    =      1387.068
<  EELEC  =    -12329.834  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       25   TIME(PS) =       0.05  TEMP(K) =   301.8  PRESS =     0.
<  Etot   =     -8313.586  EKtot   =      1908.683  EPtot      =    -10222.269
<  BOND   =        35.446  ANGLE   =        70.843  DIHED      =        73.476
<  1-4 NB =        28.888  1-4 EEL =       538.883  VDWAALS    =      1406.839
<  EELEC  =    -12376.647  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       30   TIME(PS) =       0.06  TEMP(K) =   307.8  PRESS =     0.
<  Etot   =     -8308.137  EKtot   =      1947.162  EPtot      =    -10255.299
<  BOND   =        32.860  ANGLE   =        64.449  DIHED      =        74.428
<  1-4 NB =        30.203  1-4 EEL =       534.519  VDWAALS    =      1408.103
<  EELEC  =    -12399.865  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       35   TIME(PS) =       0.07  TEMP(K) =   296.0  PRESS =     0.
<  Etot   =     -8312.353  EKtot   =      1871.985  EPtot      =    -10184.339
<  BOND   =        23.747  ANGLE   =        70.925  DIHED      =        73.514
<  1-4 NB =        30.145  1-4 EEL =       531.149  VDWAALS    =      1412.156
<  EELEC  =    -12325.977  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       40   TIME(PS) =       0.08  TEMP(K) =   300.0  PRESS =     0.
<  Etot   =     -8316.331  EKtot   =      1897.756  EPtot      =    -10214.087
<  BOND   =        27.618  ANGLE   =        63.522  DIHED      =        74.691
<  1-4 NB =        34.552  1-4 EEL =       531.048  VDWAALS    =      1411.040
<  EELEC  =    -12356.562  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       45   TIME(PS) =       0.09  TEMP(K) =   298.9  PRESS =     0.
<  Etot   =     -8320.692  EKtot   =      1890.608  EPtot      =    -10211.301
<  BOND   =        29.076  ANGLE   =        59.155  DIHED      =        74.590
<  1-4 NB =        35.567  1-4 EEL =       533.225  VDWAALS    =      1407.882
<  EELEC  =    -12350.798  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       50   TIME(PS) =       0.10  TEMP(K) =   305.2  PRESS =     0.
<  Etot   =     -8323.455  EKtot   =      1930.659  EPtot      =    -10254.114
<  BOND   =        22.640  ANGLE   =        69.817  DIHED      =        71.623
<  1-4 NB =        35.126  1-4 EEL =       535.015  VDWAALS    =      1393.391
<  EELEC  =    -12381.728  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<       A V E R A G E S   O V E R      50 S T E P S
<  NSTEP =       50   TIME(PS) =       0.10  TEMP(K) =   300.6  PRESS =     0.
<  Etot   =     -8317.366  EKtot   =      1901.322  EPtot      =    -10218.688
<  BOND   =        28.949  ANGLE   =        67.572  DIHED      =        73.819
<  1-4 NB =        31.971  1-4 EEL =       536.040  VDWAALS    =      1376.209
<  EELEC  =    -12333.251  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<       R M S  F L U C T U A T I O N S
<  NSTEP =       50   TIME(PS) =       0.10  TEMP(K) =     3.2  PRESS =     0.
<  Etot   =         6.900  EKtot   =        20.558  EPtot      =        20.606
<  BOND   =         4.608  ANGLE   =         4.103  DIHED      =         1.950
<  1-4 NB =         2.404  1-4 EEL =         3.752  VDWAALS    =        43.558
<  EELEC  =        42.130  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---
>  ** NCSU-Error ** : expected list value for key 'i', got '<EMPTY>' instead
---------------------------------------
possible FAILURE:  check monitor.txt.dif
/home/tolsan83/amber10/test/ncsu/abmd_FLOODING
1,53d0
< #
< # MD time (ps), CV #1, E_{bias} (kcal/mol)
< #
<       0.     6.231568206     0.
<       0.002     6.234804122     0.001999375
<       0.004     6.238046031     0.003998656
<       0.006     6.241400758     0.005997388
<       0.008     6.244754844     0.007995130
<       0.010     6.248257461     0.009991216
<       0.012     6.251783612     0.011985141
<       0.014     6.255299816     0.013976440
<       0.016     6.258596155     0.015965453
<       0.018     6.261494385     0.017953170
<       0.020     6.263588023     0.019942487
<       0.022     6.264792595     0.021935409
<       0.024     6.265061686     0.023933376
<       0.026     6.264482951     0.025936299
<       0.028     6.263601646     0.027940805
<       0.030     6.262856932     0.029944360
<       0.032     6.262421106     0.031946218
<       0.034     6.262561675     0.033945183
<       0.036     6.263104640     0.035941983
<       0.038     6.263729697     0.037938077
<       0.040     6.264547443     0.039932640
<       0.042     6.265499353     0.041925738
<       0.044     6.266695197     0.043916195
<       0.046     6.268210292     0.045902633
<       0.048     6.269952440     0.047884854
<       0.050     6.271997327     0.049860925
<       0.052     6.274072274     0.051833032
<       0.054     6.276233987     0.053800005
<       0.056     6.278059752     0.055768603
<       0.058     6.279348534     0.057744080
<       0.060     6.279955280     0.059731091
<       0.062     6.279874940     0.061731001
<       0.064     6.279295912     0.063740340
<       0.066     6.278360740     0.065755875
<       0.068     6.277446572     0.067770352
<       0.070     6.276590564     0.069783193
<       0.072     6.276121692     0.071789382
<       0.074     6.276142628     0.073787768
<       0.076     6.276335102     0.075783392
<       0.078     6.276811249     0.077774213
<       0.080     6.277546225     0.079760116
<       0.082     6.278241718     0.081745976
<       0.084     6.278656649     0.083736587
<       0.086     6.278701715     0.085734203
<       0.088     6.278450898     0.087737562
<       0.090     6.277772038     0.089748899
<       0.092     6.276793857     0.091764936
<       0.094     6.275522533     0.093784409
<       0.096     6.274342420     0.095800533
<       0.098     6.273405305     0.097811808
---------------------------------------
possible FAILURE:  check umbrella.ncdump.dif
/home/tolsan83/amber10/test/ncsu/abmd_FLOODING
1,25d0
< 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.,   0.0000297349,
<       0.0597045928,   0.1166473674,   0.0717906551,   0.0007809803,
<       0.,   0.,   0.,   0.,
<       0.,   0.,   0.,   0.,
<       0.,   0.,   0.,   0.,
<       0. ;
< }
---------------------------------------
possible FAILURE:  check mdout.dif
/home/tolsan83/amber10/test/ncsu/abmd_UMBRELLA
104,238c104
<  NCSU : () () () () () () () () () ()   A. B. M. D.  () () () () () () () () ()
<  NCSU :
<  NCSU : mode = UMBRELLA
<  NCSU :
<  NCSU : CV #1
<  NCSU :   type = 'MULTI_RMSD'
<  NCSU : <> group <> #1:
<  NCSU : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA],
<  NCSU :    29 [C], 31 [N], 33 [CA], 41 [C], 43 [N],
<  NCSU :    53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C],
<  NCSU :    72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA],
<  NCSU :    91 [C], 93 [N], 95 [CA], 105 [C], 107 [N],
<  NCSU :    109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C])
<  NCSU : reference coordinates :
<  NCSU :        1 :   -0.29,    4.03,  -17.15
<  NCSU :        5 :    0.47,    4.46,  -16.54
<  NCSU :        8 :    1.93,    4.40,  -16.85
<  NCSU :       10 :    2.78,    4.75,  -16.00
<  NCSU :       12 :    4.24,    4.79,  -16.12
<  NCSU :       29 :    4.93,    4.19,  -14.90
<  NCSU :       31 :    6.13,    3.68,  -15.06
<  NCSU :       33 :    6.94,    3.05,  -14.02
<  NCSU :       41 :    8.38,    3.58,  -14.03
<  NCSU :       43 :    8.73,    4.54,  -13.17
<  NCSU :       53 :   10.07,    5.08,  -13.08
<  NCSU :       55 :   11.16,    4.09,  -12.71
<  NCSU :       57 :   10.86,    2.98,  -12.09
<  NCSU :       59 :   11.82,    1.94,  -11.73
<  NCSU :       70 :   12.35,    1.16,  -12.92
<  NCSU :       72 :   11.67,    1.15,  -14.03
<  NCSU :       74 :   12.09,    0.51,  -15.29
<  NCSU :       84 :   12.13,    1.46,  -16.47
<  NCSU :       86 :   11.48,    2.61,  -16.39
<  NCSU :       88 :   11.36,    3.58,  -17.46
<  NCSU :       91 :   10.38,    3.19,  -18.54
<  NCSU :       93 :    9.30,    2.52,  -18.22
<  NCSU :       95 :    8.35,    1.93,  -19.17
<  NCSU :      105 :    6.91,    2.35,  -18.92
<  NCSU :      107 :    6.06,    2.25,  -19.92
<  NCSU :      109 :    4.66,    2.61,  -19.91
<  NCSU :      129 :    3.76,    1.41,  -19.92
<  NCSU :      131 :    2.69,    1.45,  -19.46
<  NCSU :      133 :    1.69,    0.44,  -19.40
<  NCSU :      136 :    0.61,    0.77,  -18.87
<  NCSU :
<  NCSU : monitor_file = monitor.txt
<  NCSU : monitor_freq = 1 (0.002 ps)
<  NCSU : umbrella_file = umbrella.nc (loaded)
<  NCSU :
<  NCSU : umbrella discretization (unchanged) :
<  NCSU : CV #1 not periodic, 41 points, min/max = 0./10.00000
<  NCSU :
<  NCSU : () () () () () () () () () () () () () () () () () () () () () () () ()
<  ---------------------------------------------------
<  APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
<  using   5000. points per unit in tabled values
<  TESTING RELATIVE ERROR over r ranging from 0. to cutoff
<  ---------------------------------------------------
<  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.
<  ------------------------------------------------------------------------------
<  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.
<  ------------------------------------------------------------------------------
<  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.
<  ------------------------------------------------------------------------------
<  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.
<  ------------------------------------------------------------------------------
<  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.
<  ------------------------------------------------------------------------------
<  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.
<  ------------------------------------------------------------------------------
<  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.
<  ------------------------------------------------------------------------------
<  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.
<  ------------------------------------------------------------------------------
<  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.
<  ------------------------------------------------------------------------------
<  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.
<  ------------------------------------------------------------------------------
<       A V E R A G E S   O V E R      50 S T E P S
<  NSTEP =       50   TIME(PS) =       0.10  TEMP(K) =   300.6  PRESS =     0.
<  Etot   =     -8317.367  EKtot   =      1901.321  EPtot      =    -10218.689
<  BOND   =        28.948  ANGLE   =        67.572  DIHED      =        73.819
<  1-4 NB =        31.971  1-4 EEL =       536.040  VDWAALS    =      1376.209
<  EELEC  =    -12333.252  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<       R M S  F L U C T U A T I O N S
<  NSTEP =       50   TIME(PS) =       0.10  TEMP(K) =     3.2  PRESS =     0.
<  Etot   =         6.900  EKtot   =        20.558  EPtot      =        20.606
<  BOND   =         4.608  ANGLE   =         4.103  DIHED      =         1.950
<  1-4 NB =         2.404  1-4 EEL =         3.752  VDWAALS    =        43.558
<  EELEC  =        42.131  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---
>  ** NCSU-Error ** : expected list value for key 'i', got '<EMPTY>' instead
---------------------------------------
possible FAILURE:  check monitor.txt.dif
/home/tolsan83/amber10/test/ncsu/abmd_UMBRELLA
1,53d0
< #
< # MD time (ps), CV #1
< #
<       0.     6.231568206
<       0.002     6.234803892
<       0.004     6.238045375
<       0.006     6.241399527
<       0.008     6.244752936
<       0.010     6.248254815
<       0.012     6.251780200
<       0.014     6.255295631
<       0.016     6.258591202
<       0.018     6.261488676
<       0.020     6.263581573
<       0.022     6.264785426
<       0.024     6.265053824
<       0.026     6.264474423
<       0.028     6.263592480
<       0.030     6.262847150
<       0.032     6.262410727
<       0.034     6.262550711
<       0.036     6.263093100
<       0.038     6.263717589
<       0.040     6.264534775
<       0.042     6.265486138
<       0.044     6.266681447
<       0.046     6.268196027
<       0.048     6.269937681
<       0.050     6.271982101
<       0.052     6.274056614
<       0.054     6.276217928
<       0.056     6.278043334
<       0.058     6.279331801
<       0.060     6.279938275
<       0.062     6.279857708
<       0.064     6.279278493
<       0.066     6.278343167
<       0.068     6.277428866
<       0.070     6.276572747
<       0.072     6.276103783
<       0.074     6.276124642
<       0.076     6.276317050
<       0.078     6.276793145
<       0.080     6.277528091
<       0.082     6.278223579
<       0.084     6.278638529
<       0.086     6.278683627
<       0.088     6.278432847
<       0.090     6.277754025
<       0.092     6.276775880
<       0.094     6.275504583
<       0.096     6.274324488
<       0.098     6.273387387
---------------------------------------
possible FAILURE:  check mdout.dif
/home/tolsan83/amber10/test/ncsu/smd
104,237c104
<  NCSU :  *  *  *  *  *  *  *  *  S T E E R E D  M.D.  *  *  *  *  *  *  *  *  *
<  NCSU :
<  NCSU : output_file = smd.txt
<  NCSU : output_freq = 1 (0.002 ps)
<  NCSU :
<  NCSU : CV #1
<  NCSU :
<  NCSU :  <> path = (6.231, 5.000)
<  NCSU :  <> harm = (0.000, 10.000, 20.000, 30.000,
<  NCSU :      40.000, 50.000, 50.000, 50.000, 50.000)
<  NCSU :
<  NCSU :   type = 'MULTI_RMSD'
<  NCSU : <> group <> #1:
<  NCSU : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA],
<  NCSU :    29 [C], 31 [N], 33 [CA], 41 [C], 43 [N],
<  NCSU :    53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C],
<  NCSU :    72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA],
<  NCSU :    91 [C], 93 [N], 95 [CA], 105 [C], 107 [N],
<  NCSU :    109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C])
<  NCSU : reference coordinates :
<  NCSU :        1 :   -0.29,    4.03,  -17.15
<  NCSU :        5 :    0.47,    4.46,  -16.54
<  NCSU :        8 :    1.93,    4.40,  -16.85
<  NCSU :       10 :    2.78,    4.75,  -16.00
<  NCSU :       12 :    4.24,    4.79,  -16.12
<  NCSU :       29 :    4.93,    4.19,  -14.90
<  NCSU :       31 :    6.13,    3.68,  -15.06
<  NCSU :       33 :    6.94,    3.05,  -14.02
<  NCSU :       41 :    8.38,    3.58,  -14.03
<  NCSU :       43 :    8.73,    4.54,  -13.17
<  NCSU :       53 :   10.07,    5.08,  -13.08
<  NCSU :       55 :   11.16,    4.09,  -12.71
<  NCSU :       57 :   10.86,    2.98,  -12.09
<  NCSU :       59 :   11.82,    1.94,  -11.73
<  NCSU :       70 :   12.35,    1.16,  -12.92
<  NCSU :       72 :   11.67,    1.15,  -14.03
<  NCSU :       74 :   12.09,    0.51,  -15.29
<  NCSU :       84 :   12.13,    1.46,  -16.47
<  NCSU :       86 :   11.48,    2.61,  -16.39
<  NCSU :       88 :   11.36,    3.58,  -17.46
<  NCSU :       91 :   10.38,    3.19,  -18.54
<  NCSU :       93 :    9.30,    2.52,  -18.22
<  NCSU :       95 :    8.35,    1.93,  -19.17
<  NCSU :      105 :    6.91,    2.35,  -18.92
<  NCSU :      107 :    6.06,    2.25,  -19.92
<  NCSU :      109 :    4.66,    2.61,  -19.91
<  NCSU :      129 :    3.76,    1.41,  -19.92
<  NCSU :      131 :    2.69,    1.45,  -19.46
<  NCSU :      133 :    1.69,    0.44,  -19.40
<  NCSU :      136 :    0.61,    0.77,  -18.87
<  NCSU :
<  NCSU :  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *  *
<  ---------------------------------------------------
<  APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
<  using   5000. points per unit in tabled values
<  TESTING RELATIVE ERROR over r ranging from 0. to cutoff
<  ---------------------------------------------------
<  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.
<  ------------------------------------------------------------------------------
<  NSTEP =       10   TIME(PS) =       0.02  TEMP(K) =   303.1  PRESS =     0.
<  Etot   =     -8329.346  EKtot   =      1917.153  EPtot      =    -10246.499
<  BOND   =        25.270  ANGLE   =        68.103  DIHED      =        73.105
<  1-4 NB =        34.018  1-4 EEL =       541.646  VDWAALS    =      1326.260
<  EELEC  =    -12314.903  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       15   TIME(PS) =       0.03  TEMP(K) =   297.2  PRESS =     0.
<  Etot   =     -8320.093  EKtot   =      1879.646  EPtot      =    -10199.740
<  BOND   =        25.714  ANGLE   =        67.693  DIHED      =        76.294
<  1-4 NB =        31.498  1-4 EEL =       535.070  VDWAALS    =      1359.514
<  EELEC  =    -12295.524  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       20   TIME(PS) =       0.04  TEMP(K) =   299.1  PRESS =     0.
<  Etot   =     -8311.974  EKtot   =      1891.986  EPtot      =    -10203.960
<  BOND   =        32.814  ANGLE   =        68.224  DIHED      =        72.902
<  1-4 NB =        28.418  1-4 EEL =       536.508  VDWAALS    =      1387.057
<  EELEC  =    -12329.884  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       25   TIME(PS) =       0.05  TEMP(K) =   301.7  PRESS =     0.
<  Etot   =     -8313.697  EKtot   =      1908.548  EPtot      =    -10222.246
<  BOND   =        35.406  ANGLE   =        70.794  DIHED      =        73.449
<  1-4 NB =        28.956  1-4 EEL =       539.144  VDWAALS    =      1406.785
<  EELEC  =    -12376.783  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       30   TIME(PS) =       0.06  TEMP(K) =   307.8  PRESS =     0.
<  Etot   =     -8308.410  EKtot   =      1947.056  EPtot      =    -10255.467
<  BOND   =        32.447  ANGLE   =        64.351  DIHED      =        74.405
<  1-4 NB =        30.346  1-4 EEL =       535.080  VDWAALS    =      1408.068
<  EELEC  =    -12400.167  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       35   TIME(PS) =       0.07  TEMP(K) =   296.0  PRESS =     0.
<  Etot   =     -8312.175  EKtot   =      1872.148  EPtot      =    -10184.323
<  BOND   =        23.620  ANGLE   =        70.461  DIHED      =        73.453
<  1-4 NB =        30.418  1-4 EEL =       532.167  VDWAALS    =      1412.069
<  EELEC  =    -12326.513  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       40   TIME(PS) =       0.08  TEMP(K) =   300.1  PRESS =     0.
<  Etot   =     -8315.722  EKtot   =      1898.261  EPtot      =    -10213.983
<  BOND   =        27.271  ANGLE   =        63.010  DIHED      =        74.567
<  1-4 NB =        35.060  1-4 EEL =       532.736  VDWAALS    =      1410.915
<  EELEC  =    -12357.545  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       45   TIME(PS) =       0.09  TEMP(K) =   299.0  PRESS =     0.
<  Etot   =     -8319.835  EKtot   =      1891.206  EPtot      =    -10211.041
<  BOND   =        28.195  ANGLE   =        58.952  DIHED      =        74.489
<  1-4 NB =        36.331  1-4 EEL =       535.683  VDWAALS    =      1407.683
<  EELEC  =    -12352.377  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       50   TIME(PS) =       0.10  TEMP(K) =   305.2  PRESS =     0.
<  Etot   =     -8321.773  EKtot   =      1930.709  EPtot      =    -10252.483
<  BOND   =        22.445  ANGLE   =        69.872  DIHED      =        71.349
<  1-4 NB =        36.237  1-4 EEL =       538.154  VDWAALS    =      1393.610
<  EELEC  =    -12384.152  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<       A V E R A G E S   O V E R      50 S T E P S
<  NSTEP =       50   TIME(PS) =       0.10  TEMP(K) =   300.6  PRESS =     0.
<  Etot   =     -8317.155  EKtot   =      1901.420  EPtot      =    -10218.575
<  BOND   =        28.736  ANGLE   =        67.445  DIHED      =        73.769
<  1-4 NB =        32.212  1-4 EEL =       536.834  VDWAALS    =      1376.174
<  EELEC  =    -12333.749  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<       R M S  F L U C T U A T I O N S
<  NSTEP =       50   TIME(PS) =       0.10  TEMP(K) =     3.2  PRESS =     0.
<  Etot   =         6.819  EKtot   =        20.478  EPtot      =        20.568
<  BOND   =         4.595  ANGLE   =         4.127  DIHED      =         1.957
<  1-4 NB =         2.612  1-4 EEL =         3.259  VDWAALS    =        43.525
<  EELEC  =        42.433  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---
>  ** NCSU-Error ** : expected list value for key 'i', got '<EMPTY>' instead
---------------------------------------
possible FAILURE:  check smd.txt.dif
/home/tolsan83/amber10/test/ncsu/smd
1,56d0
< #
< # MD time (ps), CV, handle_position, spring_constant, work
< #
<       0.       6.2315682       6.2315682       0.       0.
<       0.002       6.2348041       6.2301100       0.4710400       0.0000068
<       0.004       6.2380460       6.2258143       1.7203200       0.0001502
<       0.006       6.2414006       6.2187993       3.5020800       0.0009567
<       0.008       6.2447542       6.2091832       5.5705600       0.0035986
<       0.010       6.2482556       6.1970843       7.6800000       0.0099365
<       0.012       6.2517789       6.1826207       9.5846400       0.0221270
<       0.014       6.2552896       6.1659108      11.2000000       0.0424810
<       0.016       6.2585766       6.1470727      12.8000000       0.0752996
<       0.018       6.2614603       6.1262247      14.4000000       0.1251078
<       0.020       6.2635324       6.1034851      16.0000000       0.1968568
<       0.022       6.2647066       6.0789719      17.6000000       0.2959066
<       0.024       6.2649343       6.0528036      19.2000000       0.4279681
<       0.026       6.2643008       6.0250982      20.8000000       0.5990860
<       0.028       6.2633488       5.9959741      22.4000000       0.8159447
<       0.030       6.2625146       5.9655494      24.0000000       1.0860257
<       0.032       6.2619672       5.9339425      25.6000000       1.4174487
<       0.034       6.2619709       5.9012714      27.2000000       1.8189766
<       0.036       6.2623477       5.8676545      28.8000000       2.2995752
<       0.038       6.2627737       5.8332100      30.4000000       2.8678641
<       0.040       6.2633554       5.7980562      32.0000000       3.5323127
<       0.042       6.2640303       5.7623111      33.6000000       4.3010953
<       0.044       6.2649040       5.7260932      35.2000000       5.1820834
<       0.046       6.2660473       5.6895205      36.8000000       6.1827769
<       0.048       6.2673634       5.6527114      38.4000000       7.3098850
<       0.050       6.2689229       5.6157841      40.0000000       8.5693221
<       0.052       6.2704476       5.5788567      41.7075200       9.9926235
<       0.054       6.2719883       5.5420476      43.5481600      11.5988894
<       0.056       6.2731156       5.5054750      45.3990400      13.3627845
<       0.058       6.2736219       5.4692570      47.1372800      15.2428206
<       0.060       6.2733562       5.4335120      48.6400000      17.1805232
<       0.062       6.2723088       5.3983581      49.7843200      19.1003075
<       0.064       6.2706654       5.3639136      50.4646400      20.9173815
<       0.066       6.2685679       5.3302967      50.7257600      22.6014462
<       0.068       6.2663943       5.2976257      50.6899200      24.1642946
<       0.070       6.2641845       5.2660187      50.4800000      25.6320744
<       0.072       6.2622712       5.2355940      50.2188800      27.0452917
<       0.074       6.2607601       5.2064699      50.0294400      28.4588910
<       0.076       6.2593363       5.1787645      50.0000000      29.9208112
<       0.078       6.2581160       5.1525962      50.0000000      31.3509721
<       0.080       6.2570812       5.1280830      50.0000000      32.7203480
<       0.082       6.2559396       5.1053434      50.0000000      34.0162789
<       0.084       6.2544557       5.0844954      50.0000000      35.2257522
<       0.086       6.2525421       5.0656573      50.0000000      36.3357124
<       0.088       6.2502700       5.0489474      50.0000000      37.3333811
<       0.090       6.2474976       5.0344839      50.0000000      38.2063771
<       0.092       6.2443438       5.0223849      50.0000000      38.9428910
<       0.094       6.2408099       5.0127689      50.0000000      39.5318761
<       0.096       6.2372871       5.0057538      50.0000000      39.9632248
<       0.098       6.2339445       5.0014581      50.0000000      40.2278426
< #
< # <> total work done:    40.227842642
< #
---------------------------------------
possible FAILURE:  check mdout.dif
/home/tolsan83/amber10/test/ncsu/pmd
104,232c104
<  NCSU : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ P I N N E D  M.D. ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~
<  NCSU :
<  NCSU : output_file = pmd.txt
<  NCSU : output_freq = 1 (0.002 ps)
<  NCSU :
<  NCSU : CV #1 << anchor : position = 6.00000, strength = 10.00000 >>
<  NCSU :   type = 'MULTI_RMSD'
<  NCSU : <> group <> #1:
<  NCSU : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA],
<  NCSU :    29 [C], 31 [N], 33 [CA], 41 [C], 43 [N],
<  NCSU :    53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C],
<  NCSU :    72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA],
<  NCSU :    91 [C], 93 [N], 95 [CA], 105 [C], 107 [N],
<  NCSU :    109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C])
<  NCSU : reference coordinates :
<  NCSU :        1 :   -0.29,    4.03,  -17.15
<  NCSU :        5 :    0.47,    4.46,  -16.54
<  NCSU :        8 :    1.93,    4.40,  -16.85
<  NCSU :       10 :    2.78,    4.75,  -16.00
<  NCSU :       12 :    4.24,    4.79,  -16.12
<  NCSU :       29 :    4.93,    4.19,  -14.90
<  NCSU :       31 :    6.13,    3.68,  -15.06
<  NCSU :       33 :    6.94,    3.05,  -14.02
<  NCSU :       41 :    8.38,    3.58,  -14.03
<  NCSU :       43 :    8.73,    4.54,  -13.17
<  NCSU :       53 :   10.07,    5.08,  -13.08
<  NCSU :       55 :   11.16,    4.09,  -12.71
<  NCSU :       57 :   10.86,    2.98,  -12.09
<  NCSU :       59 :   11.82,    1.94,  -11.73
<  NCSU :       70 :   12.35,    1.16,  -12.92
<  NCSU :       72 :   11.67,    1.15,  -14.03
<  NCSU :       74 :   12.09,    0.51,  -15.29
<  NCSU :       84 :   12.13,    1.46,  -16.47
<  NCSU :       86 :   11.48,    2.61,  -16.39
<  NCSU :       88 :   11.36,    3.58,  -17.46
<  NCSU :       91 :   10.38,    3.19,  -18.54
<  NCSU :       93 :    9.30,    2.52,  -18.22
<  NCSU :       95 :    8.35,    1.93,  -19.17
<  NCSU :      105 :    6.91,    2.35,  -18.92
<  NCSU :      107 :    6.06,    2.25,  -19.92
<  NCSU :      109 :    4.66,    2.61,  -19.91
<  NCSU :      129 :    3.76,    1.41,  -19.92
<  NCSU :      131 :    2.69,    1.45,  -19.46
<  NCSU :      133 :    1.69,    0.44,  -19.40
<  NCSU :      136 :    0.61,    0.77,  -18.87
<  NCSU :
<  NCSU : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~
<  ---------------------------------------------------
<  APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
<  using   5000. points per unit in tabled values
<  TESTING RELATIVE ERROR over r ranging from 0. to cutoff
<  ---------------------------------------------------
<  NSTEP =        5   TIME(PS) =       0.01  TEMP(K) =   302.6  PRESS =     0.
<  Etot   =     -8321.518  EKtot   =      1914.146  EPtot      =    -10235.665
<  BOND   =        19.066  ANGLE   =        63.597  DIHED      =        72.694
<  1-4 NB =        31.933  1-4 EEL =       541.008  VDWAALS    =      1297.272
<  EELEC  =    -12261.238  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       10   TIME(PS) =       0.02  TEMP(K) =   303.1  PRESS =     0.
<  Etot   =     -8329.410  EKtot   =      1917.121  EPtot      =    -10246.532
<  BOND   =        25.239  ANGLE   =        68.081  DIHED      =        73.111
<  1-4 NB =        34.021  1-4 EEL =       541.682  VDWAALS    =      1326.258
<  EELEC  =    -12314.926  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       15   TIME(PS) =       0.03  TEMP(K) =   297.2  PRESS =     0.
<  Etot   =     -8320.163  EKtot   =      1879.592  EPtot      =    -10199.756
<  BOND   =        25.701  ANGLE   =        67.655  DIHED      =        76.300
<  1-4 NB =        31.510  1-4 EEL =       535.120  VDWAALS    =      1359.512
<  EELEC  =    -12295.558  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       20   TIME(PS) =       0.04  TEMP(K) =   299.1  PRESS =     0.
<  Etot   =     -8312.045  EKtot   =      1891.970  EPtot      =    -10204.016
<  BOND   =        32.790  ANGLE   =        68.190  DIHED      =        72.905
<  1-4 NB =        28.426  1-4 EEL =       536.529  VDWAALS    =      1387.049
<  EELEC  =    -12329.907  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       25   TIME(PS) =       0.05  TEMP(K) =   301.7  PRESS =     0.
<  Etot   =     -8313.699  EKtot   =      1908.613  EPtot      =    -10222.312
<  BOND   =        35.390  ANGLE   =        70.794  DIHED      =        73.473
<  1-4 NB =        28.933  1-4 EEL =       539.046  VDWAALS    =      1406.802
<  EELEC  =    -12376.752  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       30   TIME(PS) =       0.06  TEMP(K) =   307.8  PRESS =     0.
<  Etot   =     -8308.264  EKtot   =      1947.081  EPtot      =    -10255.345
<  BOND   =        32.769  ANGLE   =        64.371  DIHED      =        74.423
<  1-4 NB =        30.255  1-4 EEL =       534.720  VDWAALS    =      1408.105
<  EELEC  =    -12399.991  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       35   TIME(PS) =       0.07  TEMP(K) =   295.9  PRESS =     0.
<  Etot   =     -8312.460  EKtot   =      1871.922  EPtot      =    -10184.382
<  BOND   =        23.704  ANGLE   =        70.796  DIHED      =        73.511
<  1-4 NB =        30.205  1-4 EEL =       531.380  VDWAALS    =      1412.158
<  EELEC  =    -12326.138  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       40   TIME(PS) =       0.08  TEMP(K) =   300.0  PRESS =     0.
<  Etot   =     -8316.436  EKtot   =      1897.677  EPtot      =    -10214.113
<  BOND   =        27.547  ANGLE   =        63.410  DIHED      =        74.681
<  1-4 NB =        34.627  1-4 EEL =       531.296  VDWAALS    =      1411.070
<  EELEC  =    -12356.748  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       45   TIME(PS) =       0.09  TEMP(K) =   298.9  PRESS =     0.
<  Etot   =     -8320.814  EKtot   =      1890.491  EPtot      =    -10211.305
<  BOND   =        28.980  ANGLE   =        59.062  DIHED      =        74.581
<  1-4 NB =        35.651  1-4 EEL =       533.488  VDWAALS    =      1407.950
<  EELEC  =    -12351.019  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<  NSTEP =       50   TIME(PS) =       0.10  TEMP(K) =   305.2  PRESS =     0.
<  Etot   =     -8323.558  EKtot   =      1930.495  EPtot      =    -10254.053
<  BOND   =        22.605  ANGLE   =        69.799  DIHED      =        71.611
<  1-4 NB =        35.212  1-4 EEL =       535.279  VDWAALS    =      1393.425
<  EELEC  =    -12381.986  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<       A V E R A G E S   O V E R      50 S T E P S
<  NSTEP =       50   TIME(PS) =       0.10  TEMP(K) =   300.6  PRESS =     0.
<  Etot   =     -8317.459  EKtot   =      1901.250  EPtot      =    -10218.709
<  BOND   =        28.897  ANGLE   =        67.515  DIHED      =        73.817
<  1-4 NB =        32.014  1-4 EEL =       536.190  VDWAALS    =      1376.216
<  EELEC  =    -12333.361  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
<       R M S  F L U C T U A T I O N S
<  NSTEP =       50   TIME(PS) =       0.10  TEMP(K) =     3.2  PRESS =     0.
<  Etot   =         6.879  EKtot   =        20.551  EPtot      =        20.601
<  BOND   =         4.599  ANGLE   =         4.105  DIHED      =         1.952
<  1-4 NB =         2.411  1-4 EEL =         3.676  VDWAALS    =        43.564
<  EELEC  =        42.185  EHBOND  =         0.  RESTRAINT  =         0.
<  ------------------------------------------------------------------------------
< --------------------------------------------------------------------------------
<    5.  TIMINGS
< --------------------------------------------------------------------------------
---
>  ** NCSU-Error ** : expected list value for key 'i', got '<EMPTY>' instead
---------------------------------------
possible FAILURE:  check pmd.txt.dif
/home/tolsan83/amber10/test/ncsu/pmd
1,55d0
< # = NCSU%PMD ==================================================================
< #   << anchor(1) : position = 6.00000, strength = 10.00000 >>
< # -----------------------------------------------------------------------------
< # MD time (ps), CV(1:1)
< # =============================================================================
<       0.       6.2315682
<       0.002       6.2347940
<       0.004       6.2380163
<       0.006       6.2413428
<       0.008       6.2446613
<       0.010       6.2481220
<       0.012       6.2516006
<       0.014       6.2550639
<       0.016       6.2583022
<       0.018       6.2611371
<       0.020       6.2631620
<       0.022       6.2642928
<       0.024       6.2644832
<       0.026       6.2638217
<       0.028       6.2628538
<       0.030       6.2620193
<       0.032       6.2614905
<       0.034       6.2615353
<       0.036       6.2619796
<       0.038       6.2625035
<       0.040       6.2632176
<       0.042       6.2640639
<       0.044       6.2651523
<       0.046       6.2665584
<       0.048       6.2681902
<       0.050       6.2701233
<       0.052       6.2720848
<       0.054       6.2741316
<       0.056       6.2758406
<       0.058       6.2770110
<       0.060       6.2774978
<       0.062       6.2772963
<       0.064       6.2765949
<       0.066       6.2755364
<       0.068       6.2744975
<       0.070       6.2735161
<       0.072       6.2729217
<       0.074       6.2728166
<       0.076       6.2728828
<       0.078       6.2732327
<       0.080       6.2738428
<       0.082       6.2744153
<       0.084       6.2747092
<       0.086       6.2746341
<       0.088       6.2742629
<       0.090       6.2734620
<       0.092       6.2723595
<       0.094       6.2709609
<       0.096       6.2696511
<       0.098       6.2685841
---------------------------------------
possible FAILURE:  check Li.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check Na.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check K.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check Rb.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check Cs.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check F.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check Cl.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check IM.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check Br.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check I.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check MG.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check Ca.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check Zn.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check tp3.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check ile.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check leu.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check val.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check phe.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check trp.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check hid.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check hie.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check nhe.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check tyr.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check ser.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check thr.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check cys.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check cyx.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check met.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check lyn.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check ash.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check glh.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check asn.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check gln.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check nma.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check alabk.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check glybk.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check probk.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check da.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check dc.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check dg.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check dt.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check ru.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check arg.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check asp.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check cym.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check glu.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check hip.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check lys.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check dap.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check da3p.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check da5p.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check danp.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check rap.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check ra3p.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check ra5p.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check ranp.out.dif
/home/tolsan83/amber10/test/pbsa_radi
---------------------------------------
possible FAILURE:  check mdout.pbsa_decres.dif
/home/tolsan83/amber10/test/pbsa_decres
---------------------------------------
possible FAILURE:  check mdout.pbsa_decpw.dif
/home/tolsan83/amber10/test/pbsa_decpw
---------------------------------------
possible FAILURE:  check first.pdb.dif
/home/tolsan83/amber10/test/ambpdb_first_protein
2147c2147
< HETATM 2145  X   BMH G  62      29.312  38.819  37.740  0.  0.   62 N
---
> HETATM 2145  X   BMH G  62      29.313  38.819  37.740  0.  0.   62 N
---------------------------------------
possible FAILURE:  check first.pdb.dif
/home/tolsan83/amber10/test/ambpdb_first_rna
2493c2493
< HETATM 2491  X   BMH G   8      23.812   6.343 -13.815  0.  0.    8 N
---
> HETATM 2491  X   BMH G   8      23.813   6.343 -13.815  0.  0.    8 N
2588c2588
< HETATM 2586  X   BMH G  39      15.716  26.812 -17.572  0.  0.   39 N
---
> HETATM 2586  X   BMH G  39      15.716  26.813 -17.572  0.  0.   39 N
2734c2734
< HETATM 2732  X   BMH G  88     -20.948  -1.812  -9.912  0.  0.   88 N
---
> HETATM 2732  X   BMH G  88     -20.948  -1.813  -9.912  0.  0.   88 N
---------------------------------------
