Reading parm file (gbrna.prmtop) title: PDB 5DNB, Dickerson decamer old prmtop format => using old algorithm for GB parms mm_options: ntpr=100 mm_options: gb=1 mm_options: kappa=0.10395 mm_options: cut=99.0 mm_options: diel=C mm_options: tempi=300. mm_options: rattle=1 iter Total bad vdW elect. cons. genBorn frms ff: 0 -4107.50 906.22 -192.79 -137.96 0.00 -4682.97 1.93e+01 md: 1 0.001 384.87 -4176.22 -3791.35 314.41 md: 10 0.010 371.06 -4162.38 -3791.32 303.13 md: 20 0.020 393.46 -4184.93 -3791.47 321.43 md: 30 0.030 394.83 -4186.30 -3791.47 322.54 md: 40 0.040 376.12 -4167.50 -3791.38 307.26 md: 50 0.050 361.85 -4153.13 -3791.29 295.60 md: 60 0.060 362.82 -4154.12 -3791.30 296.39 md: 70 0.070 379.95 -4171.36 -3791.41 310.39 md: 80 0.080 387.56 -4179.01 -3791.45 316.60 md: 90 0.090 383.75 -4175.17 -3791.42 313.50 ff: 100 -4179.81 782.97 -186.32 -93.25 0.00 -4683.22 1.34e+01 md: 100 0.100 388.39 -4179.81 -3791.42 317.28 md: 110 0.110 361.29 -4152.62 -3791.33 295.15 md: 120 0.120 376.73 -4168.13 -3791.40 307.76 md: 130 0.130 397.05 -4188.50 -3791.45 324.36 md: 140 0.140 385.67 -4177.05 -3791.39 315.06 md: 150 0.150 378.55 -4169.87 -3791.32 309.25 md: 160 0.160 375.66 -4166.98 -3791.32 306.89 md: 170 0.170 381.26 -4172.69 -3791.43 311.46 md: 180 0.180 386.78 -4178.29 -3791.52 315.97 md: 190 0.190 381.73 -4173.11 -3791.38 311.84 ff: 200 -4165.64 796.11 -168.74 -76.67 0.00 -4716.34 1.36e+01 md: 200 0.200 374.39 -4165.64 -3791.24 305.85 md: 210 0.210 371.63 -4162.90 -3791.27 303.59 md: 220 0.220 389.74 -4181.22 -3791.48 318.38 md: 230 0.230 395.15 -4186.67 -3791.52 322.81 md: 240 0.240 372.77 -4164.11 -3791.35 304.52 md: 250 0.250 386.06 -4177.45 -3791.39 315.38 md: 260 0.260 393.36 -4184.80 -3791.43 321.35 md: 270 0.270 375.93 -4167.29 -3791.36 307.10 md: 280 0.280 372.33 -4163.61 -3791.27 304.17 md: 290 0.290 398.27 -4189.74 -3791.47 325.35 ff: 300 -4157.77 796.41 -168.27 -55.13 0.00 -4730.78 1.43e+01 md: 300 0.300 366.36 -4157.77 -3791.41 299.29 md: 310 0.310 387.54 -4178.97 -3791.42 316.59 md: 320 0.320 392.55 -4183.88 -3791.33 320.68 md: 330 0.330 369.78 -4161.03 -3791.25 302.08 md: 340 0.340 392.08 -4183.44 -3791.36 320.30 md: 350 0.350 375.08 -4166.34 -3791.27 306.41 md: 360 0.360 377.89 -4169.31 -3791.43 308.70 md: 370 0.370 389.75 -4181.23 -3791.48 318.39 md: 380 0.380 396.46 -4187.94 -3791.49 323.87 md: 390 0.390 359.40 -4150.60 -3791.20 293.60 ff: 400 -4166.21 776.23 -157.70 -66.61 0.00 -4718.13 1.37e+01 md: 400 0.400 374.94 -4166.21 -3791.26 306.30 md: 410 0.410 401.17 -4192.66 -3791.49 327.73 md: 420 0.420 380.78 -4172.26 -3791.48 311.07 md: 430 0.430 391.34 -4182.85 -3791.50 319.70 md: 440 0.440 379.02 -4170.38 -3791.36 309.63 md: 450 0.450 394.06 -4185.49 -3791.43 321.92 md: 460 0.460 381.58 -4172.91 -3791.34 311.72 md: 470 0.470 383.45 -4174.83 -3791.38 313.25 md: 480 0.480 387.09 -4178.45 -3791.37 316.22 md: 490 0.490 391.33 -4182.72 -3791.38 319.69 ff: 500 -4161.60 769.21 -147.13 -56.09 0.00 -4727.59 1.35e+01 md: 500 0.500 370.27 -4161.60 -3791.32 302.48 md: 510 0.510 375.74 -4167.09 -3791.35 306.95 md: 520 0.520 393.77 -4185.17 -3791.40 321.68 md: 530 0.530 388.97 -4180.28 -3791.31 317.76 md: 540 0.540 362.74 -4153.96 -3791.22 296.33 md: 550 0.550 371.54 -4162.94 -3791.40 303.52 md: 560 0.560 384.89 -4176.36 -3791.48 314.42 md: 570 0.570 380.23 -4171.66 -3791.42 310.62 md: 580 0.580 380.43 -4171.81 -3791.38 310.78 md: 590 0.590 394.99 -4186.46 -3791.47 322.67 ff: 600 -4176.82 761.85 -169.90 -27.55 0.00 -4741.22 1.32e+01 md: 600 0.600 385.38 -4176.82 -3791.44 314.82 md: 610 0.610 371.97 -4163.31 -3791.34 303.87 md: 620 0.620 363.35 -4154.63 -3791.28 296.83 md: 630 0.630 395.35 -4186.91 -3791.56 322.97 md: 640 0.640 382.41 -4173.91 -3791.50 312.40 md: 650 0.650 380.74 -4172.04 -3791.30 311.03 md: 660 0.660 377.41 -4168.54 -3791.13 308.32 md: 670 0.670 383.72 -4175.03 -3791.31 313.47 md: 680 0.680 387.83 -4179.32 -3791.49 316.83 md: 690 0.690 386.50 -4177.98 -3791.48 315.74 ff: 700 -4166.02 772.51 -161.73 -85.77 0.00 -4691.04 1.32e+01 md: 700 0.700 374.61 -4166.02 -3791.41 306.03 md: 710 0.710 377.95 -4169.34 -3791.39 308.76 md: 720 0.720 393.71 -4185.16 -3791.44 321.63 md: 730 0.730 382.54 -4173.93 -3791.39 312.50 md: 740 0.740 373.04 -4164.39 -3791.35 304.75 md: 750 0.750 375.12 -4166.50 -3791.39 306.44 md: 760 0.760 386.18 -4177.64 -3791.46 315.48 md: 770 0.770 389.44 -4180.89 -3791.45 318.14 md: 780 0.780 380.66 -4172.07 -3791.41 310.97 md: 790 0.790 387.54 -4178.93 -3791.39 316.59 ff: 800 -4172.31 770.62 -159.90 -112.84 0.00 -4670.18 1.30e+01 md: 800 0.800 381.00 -4172.31 -3791.31 311.24 md: 810 0.810 388.41 -4179.74 -3791.32 317.30 md: 820 0.820 385.52 -4176.84 -3791.31 314.94 md: 830 0.830 393.25 -4184.67 -3791.41 321.26 md: 840 0.840 395.80 -4187.27 -3791.47 323.34 md: 850 0.850 390.44 -4181.88 -3791.44 318.96 md: 860 0.860 388.44 -4179.81 -3791.38 317.32 md: 870 0.870 378.54 -4169.86 -3791.32 309.24 md: 880 0.880 377.27 -4168.59 -3791.32 308.20 md: 890 0.890 376.67 -4168.11 -3791.44 307.71 ff: 900 -4143.00 812.81 -159.88 -124.73 0.00 -4671.21 1.37e+01 md: 900 0.900 351.58 -4143.00 -3791.43 287.21 md: 910 0.910 370.88 -4162.33 -3791.45 302.98 md: 920 0.920 353.32 -4144.55 -3791.23 288.63 md: 930 0.930 368.31 -4159.60 -3791.29 300.88 md: 940 0.940 370.40 -4161.80 -3791.40 302.59 md: 950 0.950 364.77 -4156.23 -3791.47 297.98 md: 960 0.960 374.00 -4165.38 -3791.38 305.53 md: 970 0.970 374.58 -4165.91 -3791.33 306.00 md: 980 0.980 373.02 -4164.38 -3791.36 304.73 md: 990 0.990 386.78 -4178.29 -3791.51 315.97 ff:1000 -4167.85 786.14 -160.75 -114.13 0.00 -4679.11 1.34e+01 md: 1000 1.000 376.38 -4167.85 -3791.47 307.47 md returns 0; elapsed time was 99.219