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 '' 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 '' 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 '' 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 '' 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 '' 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 ---------------------------------------