CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/08/18 09:00:20 | Available memory: 31.847 GB INPUT: Reading input from '/u/sciteam/ros/scratch/salt/nowater.cpptraj' [noexitonerror] Attempting to ignore errors if possible. [parm repartitioned.topo] Reading 'repartitioned.topo' as Amber Topology [trajin TRAJ/traj.1 1 last 10] Reading 'TRAJ/traj.1' as Amber NetCDF [trajin TRAJ/traj.2 1 last 10] Reading 'TRAJ/traj.2' as Amber NetCDF [trajin TRAJ/traj.3 1 last 10] Reading 'TRAJ/traj.3' as Amber NetCDF [trajin TRAJ/traj.4 1 last 10] Reading 'TRAJ/traj.4' as Amber NetCDF [trajin TRAJ/traj.5 1 last 10] Reading 'TRAJ/traj.5' as Amber NetCDF [trajin TRAJ/traj.6 1 last 10] Reading 'TRAJ/traj.6' as Amber NetCDF [trajin TRAJ/traj.7 1 last 10] Reading 'TRAJ/traj.7' as Amber NetCDF [trajin TRAJ/traj.8 1 last 10] Reading 'TRAJ/traj.8' as Amber NetCDF [trajin TRAJ/traj.9 1 last 10] Reading 'TRAJ/traj.9' as Amber NetCDF [trajin TRAJ/traj.10 1 last 10] Reading 'TRAJ/traj.10' as Amber NetCDF [trajin TRAJ/traj.11 1 last 10] Reading 'TRAJ/traj.11' as Amber NetCDF [trajin TRAJ/traj.12 1 last 10] Reading 'TRAJ/traj.12' as Amber NetCDF [trajin TRAJ/traj.13 1 last 10] Reading 'TRAJ/traj.13' as Amber NetCDF [trajin TRAJ/traj.14 1 last 10] Reading 'TRAJ/traj.14' as Amber NetCDF [trajin TRAJ/traj.15 1 last 10] Reading 'TRAJ/traj.15' as Amber NetCDF [trajin TRAJ/traj.16 1 last 10] Reading 'TRAJ/traj.16' as Amber NetCDF [trajin TRAJ/traj.17 1 last 10] Reading 'TRAJ/traj.17' as Amber NetCDF [trajin TRAJ/traj.18 1 last 10] Reading 'TRAJ/traj.18' as Amber NetCDF [trajin TRAJ/traj.19 1 last 10] Reading 'TRAJ/traj.19' as Amber NetCDF [trajin TRAJ/traj.20 1 last 10] Reading 'TRAJ/traj.20' as Amber NetCDF [trajin TRAJ/traj.21 1 last 10] Reading 'TRAJ/traj.21' as Amber NetCDF [trajin TRAJ/traj.22 1 last 10] Reading 'TRAJ/traj.22' as Amber NetCDF [trajin TRAJ/traj.23 1 last 10] Reading 'TRAJ/traj.23' as Amber NetCDF [trajin TRAJ/traj.24 1 last 10] Reading 'TRAJ/traj.24' as Amber NetCDF [trajin TRAJ/traj.25 1 last 10] Reading 'TRAJ/traj.25' as Amber NetCDF [trajin TRAJ/traj.26 1 last 10] Reading 'TRAJ/traj.26' as Amber NetCDF [trajin TRAJ/traj.27 1 last 10] Reading 'TRAJ/traj.27' as Amber NetCDF [trajin TRAJ/traj.28 1 last 10] Reading 'TRAJ/traj.28' as Amber NetCDF [trajin TRAJ/traj.29 1 last 10] Reading 'TRAJ/traj.29' as Amber NetCDF [trajin TRAJ/traj.30 1 last 10] Reading 'TRAJ/traj.30' as Amber NetCDF [trajin TRAJ/traj.31 1 last 10] Reading 'TRAJ/traj.31' as Amber NetCDF [trajin TRAJ/traj.32 1 last 10] Reading 'TRAJ/traj.32' as Amber NetCDF [trajin TRAJ/traj.33 1 last 10] Reading 'TRAJ/traj.33' as Amber NetCDF [trajin TRAJ/traj.34 1 last 10] Reading 'TRAJ/traj.34' as Amber NetCDF [trajin TRAJ/traj.35 1 last 10] Reading 'TRAJ/traj.35' as Amber NetCDF [trajin TRAJ/traj.36 1 last 10] Reading 'TRAJ/traj.36' as Amber NetCDF [trajin TRAJ/traj.37 1 last 10] Reading 'TRAJ/traj.37' as Amber NetCDF [trajin TRAJ/traj.38 1 last 10] Reading 'TRAJ/traj.38' as Amber NetCDF [trajin TRAJ/traj.39 1 last 10] Reading 'TRAJ/traj.39' as Amber NetCDF [trajin TRAJ/traj.40 1 last 10] Reading 'TRAJ/traj.40' as Amber NetCDF [trajin TRAJ/traj.41 1 last 10] Reading 'TRAJ/traj.41' as Amber NetCDF [trajin TRAJ/traj.42 1 last 10] Reading 'TRAJ/traj.42' as Amber NetCDF [trajin TRAJ/traj.43 1 last 10] Reading 'TRAJ/traj.43' as Amber NetCDF [trajin TRAJ/traj.44 1 last 10] Reading 'TRAJ/traj.44' as Amber NetCDF [trajin TRAJ/traj.45 1 last 10] Reading 'TRAJ/traj.45' as Amber NetCDF [trajin TRAJ/traj.46 1 last 10] Reading 'TRAJ/traj.46' as Amber NetCDF [trajin TRAJ/traj.47 1 last 10] Reading 'TRAJ/traj.47' as Amber NetCDF [trajin TRAJ/traj.48 1 last 10] Reading 'TRAJ/traj.48' as Amber NetCDF [trajin TRAJ/traj.49 1 last 10] Reading 'TRAJ/traj.49' as Amber NetCDF [trajin TRAJ/traj.50 1 last 10] Reading 'TRAJ/traj.50' as Amber NetCDF [trajin TRAJ/traj.51 1 last 10] Reading 'TRAJ/traj.51' as Amber NetCDF [trajin TRAJ/traj.52 1 last 10] Reading 'TRAJ/traj.52' as Amber NetCDF [trajin TRAJ/traj.53 1 last 10] Reading 'TRAJ/traj.53' as Amber NetCDF [trajin TRAJ/traj.54 1 last 10] Reading 'TRAJ/traj.54' as Amber NetCDF [trajin TRAJ/traj.55 1 last 10] Reading 'TRAJ/traj.55' as Amber NetCDF [trajin TRAJ/traj.56 1 last 10] Reading 'TRAJ/traj.56' as Amber NetCDF [trajin TRAJ/traj.57 1 last 10] Reading 'TRAJ/traj.57' as Amber NetCDF [trajin TRAJ/traj.58 1 last 10] Reading 'TRAJ/traj.58' as Amber NetCDF [trajin TRAJ/traj.59 1 last 10] Reading 'TRAJ/traj.59' as Amber NetCDF [trajin TRAJ/traj.60 1 last 10] Reading 'TRAJ/traj.60' as Amber NetCDF [trajin TRAJ/traj.61 1 last 10] Reading 'TRAJ/traj.61' as Amber NetCDF [trajin TRAJ/traj.62 1 last 10] Reading 'TRAJ/traj.62' as Amber NetCDF [trajin TRAJ/traj.63 1 last 10] Reading 'TRAJ/traj.63' as Amber NetCDF [trajin TRAJ/traj.64 1 last 10] Reading 'TRAJ/traj.64' as Amber NetCDF [trajin TRAJ/traj.65 1 last 10] Reading 'TRAJ/traj.65' as Amber NetCDF [trajin TRAJ/traj.66 1 last 10] Reading 'TRAJ/traj.66' as Amber NetCDF [trajin TRAJ/traj.67 1 last 10] Reading 'TRAJ/traj.67' as Amber NetCDF [trajin TRAJ/traj.68 1 last 10] Reading 'TRAJ/traj.68' as Amber NetCDF [trajin TRAJ/traj.69 1 last 10] Reading 'TRAJ/traj.69' as Amber NetCDF [trajin TRAJ/traj.70 1 last 10] Reading 'TRAJ/traj.70' as Amber NetCDF [trajin TRAJ/traj.71 1 last 10] Reading 'TRAJ/traj.71' as Amber NetCDF [trajin TRAJ/traj.72 1 last 10] Reading 'TRAJ/traj.72' as Amber NetCDF [trajin TRAJ/traj.73 1 last 10] Reading 'TRAJ/traj.73' as Amber NetCDF [trajin TRAJ/traj.74 1 last 10] Reading 'TRAJ/traj.74' as Amber NetCDF [trajin TRAJ/traj.75 1 last 10] Reading 'TRAJ/traj.75' as Amber NetCDF [trajin TRAJ/traj.76 1 last 10] Reading 'TRAJ/traj.76' as Amber NetCDF [trajin TRAJ/traj.77 1 last 10] Reading 'TRAJ/traj.77' as Amber NetCDF [trajin TRAJ/traj.78 1 last 10] Reading 'TRAJ/traj.78' as Amber NetCDF [trajin TRAJ/traj.79 1 last 10] Reading 'TRAJ/traj.79' as Amber NetCDF [trajin TRAJ/traj.80 1 last 10] Reading 'TRAJ/traj.80' as Amber NetCDF [trajin TRAJ/traj.81 1 last 10] Reading 'TRAJ/traj.81' as Amber NetCDF [trajin TRAJ/traj.82 1 last 10] Reading 'TRAJ/traj.82' as Amber NetCDF [trajin TRAJ/traj.83 1 last 10] Reading 'TRAJ/traj.83' as Amber NetCDF [trajin TRAJ/traj.84 1 last 10] Reading 'TRAJ/traj.84' as Amber NetCDF [trajin TRAJ/traj.85 1 last 10] Reading 'TRAJ/traj.85' as Amber NetCDF [trajin TRAJ/traj.86 1 last 10] Reading 'TRAJ/traj.86' as Amber NetCDF [trajin TRAJ/traj.87 1 last 10] Reading 'TRAJ/traj.87' as Amber NetCDF [trajin TRAJ/traj.88 1 last 10] Reading 'TRAJ/traj.88' as Amber NetCDF [trajin TRAJ/traj.89 1 last 10] Reading 'TRAJ/traj.89' as Amber NetCDF [trajin TRAJ/traj.90 1 last 10] Reading 'TRAJ/traj.90' as Amber NetCDF [trajin TRAJ/traj.91 1 last 10] Reading 'TRAJ/traj.91' as Amber NetCDF [trajin TRAJ/traj.92 1 last 10] Reading 'TRAJ/traj.92' as Amber NetCDF [trajin TRAJ/traj.93 1 last 10] [trajin TRAJ/traj.94 1 last 10] [trajin TRAJ/traj.95 1 last 10] [trajin TRAJ/traj.96 1 last 10] [trajin TRAJ/traj.97 1 last 10] [trajin TRAJ/traj.98 1 last 10] [trajin TRAJ/traj.99 1 last 10] [trajin TRAJ/traj.100 1 last 10] [trajin TRAJ/traj.101 1 last 10] [trajin TRAJ/traj.102 1 last 10] [trajin TRAJ/traj.103 1 last 10] [trajin TRAJ/traj.104 1 last 10] 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TRAJ/traj.495 1 last 10] [trajin TRAJ/traj.496 1 last 10] [trajin TRAJ/traj.497 1 last 10] [trajin TRAJ/traj.498 1 last 10] [trajin TRAJ/traj.499 1 last 10] [trajin TRAJ/traj.500 1 last 10] [check @1,2,3,4,5 skipbadframes silent] CHECKSTRUCTURE: Checking atoms in mask '@1,2,3,4,5'. Number of problems in each frame will be saved to set 'CHECK_00001' Checking inter-atomic and bond distances. Warnings will be printed for bond lengths > eq + 1.15 Ang and non-bond distances < 0.80 Ang. Frames with problems will be skipped. Structure warning messages will be suppressed. Parallelizing calculation with 1 threads. [autoimage] AUTOIMAGE: To box center based on center of mass, anchor is first molecule. [strip :WAT] STRIP: Stripping atoms in mask [:WAT] [rms fit :1-24] RMSD: (:1-24), reference is first frame (:1-24). Best-fit RMSD will be calculated, coords will be rotated and translated. [trajout nowater.nc netcdf] Writing 'nowater.nc' as Amber NetCDF [go] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: repartitioned.topo, 33844 atoms, 9647 res, box: Trunc. Oct., 9625 mol, 7821 solvent INPUT TRAJECTORIES (92 total): 0: 'traj.1' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 938 of 9377) 1: 'traj.2' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 911 of 9108) 2: 'traj.3' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 808 of 8078) 3: 'traj.4' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 881 of 8809) 4: 'traj.5' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 937 of 9365) 5: 'traj.6' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 938 of 9375) 6: 'traj.7' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 995 of 9942) 7: 'traj.8' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 993 of 9928) 8: 'traj.9' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 996 of 9953) 9: 'traj.10' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 997 of 9962) 10: 'traj.11' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 976 of 9752) 11: 'traj.12' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 998 of 9975) 12: 'traj.13' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 784 of 7831) 13: 'traj.14' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1000 of 9995) 14: 'traj.15' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1000 of 9991) 15: 'traj.16' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1003 of 10025) 16: 'traj.17' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1004 of 10038) 17: 'traj.18' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 999 of 9985) 18: 'traj.19' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 992 of 9914) 19: 'traj.20' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 985 of 9845) 20: 'traj.21' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 998 of 9971) 21: 'traj.22' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 999 of 9988) 22: 'traj.23' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1000 of 9994) 23: 'traj.24' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 992 of 9918) 24: 'traj.25' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 998 of 9971) 25: 'traj.26' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 805 of 8047) 26: 'traj.27' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 993 of 9926) 27: 'traj.28' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 987 of 9870) 28: 'traj.29' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 863 of 8623) 29: 'traj.30' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 993 of 9921) 30: 'traj.31' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 998 of 9974) 31: 'traj.32' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1000 of 9996) 32: 'traj.33' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1002 of 10013) 33: 'traj.34' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1132 of 11314) 34: 'traj.35' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1043 of 10430) 35: 'traj.36' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1127 of 11266) 36: 'traj.37' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1138 of 11372) 37: 'traj.38' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1132 of 11320) 38: 'traj.39' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1133 of 11327) 39: 'traj.40' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1131 of 11310) 40: 'traj.41' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1138 of 11371) 41: 'traj.42' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1115 of 11150) 42: 'traj.43' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1126 of 11258) 43: 'traj.44' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1124 of 11232) 44: 'traj.45' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1125 of 11250) 45: 'traj.46' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1138 of 11380) 46: 'traj.47' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1133 of 11322) 47: 'traj.48' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1135 of 11344) 48: 'traj.49' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1132 of 11320) 49: 'traj.50' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1114 of 11139) 50: 'traj.51' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1050 of 10492) 51: 'traj.52' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1128 of 11271) 52: 'traj.53' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1123 of 11223) 53: 'traj.54' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1133 of 11328) 54: 'traj.55' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1129 of 11288) 55: 'traj.56' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 40 of 394) 56: 'traj.57' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1124 of 11240) 57: 'traj.58' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1090 of 10898) 58: 'traj.59' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1091 of 10902) 59: 'traj.60' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1131 of 11310) 60: 'traj.61' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1126 of 11254) 61: 'traj.62' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1131 of 11305) 62: 'traj.63' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1132 of 11317) 63: 'traj.64' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1132 of 11315) 64: 'traj.65' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1132 of 11320) 65: 'traj.66' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1123 of 11229) 66: 'traj.67' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 116 of 1153) 67: 'traj.68' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 116 of 1153) 68: 'traj.69' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 115 of 1147) 69: 'traj.70' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 115 of 1145) 70: 'traj.71' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 114 of 1140) 71: 'traj.72' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 114 of 1131) 72: 'traj.73' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 114 of 1135) 73: 'traj.74' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 115 of 1143) 74: 'traj.75' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 115 of 1149) 75: 'traj.76' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 115 of 1150) 76: 'traj.77' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 115 of 1146) 77: 'traj.78' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 115 of 1149) 78: 'traj.79' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1143 of 11427) 79: 'traj.80' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1146 of 11460) 80: 'traj.81' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1141 of 11401) 81: 'traj.82' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1148 of 11471) 82: 'traj.83' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1123 of 11222) 83: 'traj.84' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1043 of 10421) 84: 'traj.85' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1133 of 11323) 85: 'traj.86' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1128 of 11271) 86: 'traj.87' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1110 of 11094) 87: 'traj.88' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1102 of 11018) 88: 'traj.89' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1135 of 11349) 89: 'traj.90' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1130 of 11298) 90: 'traj.91' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1115 of 11141) 91: 'traj.92' is a NetCDF AMBER trajectory, Parm repartitioned.topo (Trunc. Oct. box) (reading 1103 of 11028) Coordinate processing will occur on 84773 frames. OUTPUT TRAJECTORIES (1 total): 'nowater.nc' (84773 frames) is a NetCDF AMBER trajectory BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'repartitioned.topo' (4 actions): 0: [check @1,2,3,4,5 skipbadframes silent] Mask [@1,2,3,4,5] corresponds to 5 atoms. Checking 4 bonds. Imaging on. 1: [autoimage] Original box is truncated octahedron, turning on 'familiar'. Anchor molecule is 1 The following molecules are fixed to anchor: 2 9623 molecules are mobile. 2: [strip :WAT] Stripping 31284 atoms. Stripped topology: 2560 atoms, 1826 res, box: Trunc. Oct., 1804 mol 3: [rms fit :1-24] Target mask: [:1-24](758) Reference mask: [:1-24](758) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. ----- traj.1 (1-9377, 10) ----- 0% ----- traj.2 (1-9108, 10) ----- ----- traj.3 (1-8078, 10) ----- ----- traj.4 (1-8809, 10) ----- ----- traj.5 (1-9365, 10) ----- ----- traj.6 (1-9375, 10) ----- ----- traj.7 (1-9942, 10) ----- ----- traj.8 (1-9928, 10) ----- ----- traj.9 (1-9953, 10) ----- ----- traj.10 (1-9962, 10) ----- 10% ----- traj.11 (1-9752, 10) ----- ----- traj.12 (1-9975, 10) ----- ----- traj.13 (1-7831, 10) ----- ----- traj.14 (1-9995, 10) ----- ----- traj.15 (1-9991, 10) ----- ----- traj.16 (1-10025, 10) ----- ----- traj.17 (1-10038, 10) ----- ----- traj.18 (1-9985, 10) ----- 20% ----- traj.19 (1-9914, 10) ----- ----- traj.20 (1-9845, 10) ----- ----- traj.21 (1-9971, 10) ----- ----- traj.22 (1-9988, 10) ----- ----- traj.23 (1-9994, 10) ----- ----- traj.24 (1-9918, 10) ----- ----- traj.25 (1-9971, 10) ----- ----- traj.26 (1-8047, 10) ----- ----- traj.27 (1-9926, 10) ----- 30% ----- traj.28 (1-9870, 10) ----- ----- traj.29 (1-8623, 10) ----- ----- traj.30 (1-9921, 10) ----- ----- traj.31 (1-9974, 10) ----- ----- traj.32 (1-9996, 10) ----- ----- traj.33 (1-10013, 10) ----- ----- traj.34 (1-11314, 10) ----- ----- traj.35 (1-10430, 10) ----- 40% ----- traj.36 (1-11266, 10) ----- ----- traj.37 (1-11372, 10) ----- ----- traj.38 (1-11320, 10) ----- ----- traj.39 (1-11327, 10) ----- ----- traj.40 (1-11310, 10) ----- ----- traj.41 (1-11371, 10) ----- ----- traj.42 (1-11150, 10) ----- ----- traj.43 (1-11258, 10) ----- 50% ----- traj.44 (1-11232, 10) ----- ----- traj.45 (1-11250, 10) ----- ----- traj.46 (1-11380, 10) ----- ----- traj.47 (1-11322, 10) ----- ----- traj.48 (1-11344, 10) ----- ----- traj.49 (1-11320, 10) ----- ----- traj.50 (1-11139, 10) ----- 60% ----- traj.51 (1-10492, 10) ----- ----- traj.52 (1-11271, 10) ----- ----- traj.53 (1-11223, 10) ----- ----- traj.54 (1-11328, 10) ----- ----- traj.55 (1-11288, 10) ----- ----- traj.56 (1-394, 10) ----- ----- traj.57 (1-11240, 10) ----- ----- traj.58 (1-10898, 10) ----- ----- traj.59 (1-10902, 10) ----- 70% ----- traj.60 (1-11310, 10) ----- ----- traj.61 (1-11254, 10) ----- ----- traj.62 (1-11305, 10) ----- ----- traj.63 (1-11317, 10) ----- ----- traj.64 (1-11315, 10) ----- ----- traj.65 (1-11320, 10) ----- ----- traj.66 (1-11229, 10) ----- ----- traj.67 (1-1153, 10) ----- ----- traj.68 (1-1153, 10) ----- 80% ----- traj.69 (1-1147, 10) ----- ----- traj.70 (1-1145, 10) ----- ----- traj.71 (1-1140, 10) ----- ----- traj.72 (1-1131, 10) ----- ----- traj.73 (1-1135, 10) ----- ----- traj.74 (1-1143, 10) ----- ----- traj.75 (1-1149, 10) ----- ----- traj.76 (1-1150, 10) ----- ----- traj.77 (1-1146, 10) ----- ----- traj.78 (1-1149, 10) ----- ----- traj.79 (1-11427, 10) ----- ----- traj.80 (1-11460, 10) ----- ----- traj.81 (1-11401, 10) ----- ----- traj.82 (1-11471, 10) ----- ----- traj.83 (1-11222, 10) ----- ----- traj.84 (1-10421, 10) ----- ----- traj.85 (1-11323, 10) ----- 90% ----- traj.86 (1-11271, 10) ----- ----- traj.87 (1-11094, 10) ----- ----- traj.88 (1-11018, 10) ----- ----- traj.89 (1-11349, 10) ----- ----- traj.90 (1-11298, 10) ----- ----- traj.91 (1-11141, 10) ----- ----- traj.92 (1-11028, 10) ----- 100% Complete. Read 84773 frames and processed 84773 frames. TIME: Avg. throughput= 17.6237 frames / second. ACTION OUTPUT: DATASETS (2 total): CHECK_00001 "CHECK_00001" (integer), size is 84773 fit "fit" (double, rms), size is 84773 RUN TIMING: TIME: Init : 0.0004 s ( 0.00%) TIME: Trajectory Process : 4810.1677 s (100.00%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0007 s ( 0.00%) TIME: Run Total 4810.1689 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 4819.3927 seconds. -------------------------------------------------------------------------------- To cite CPPTRAJ use: Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem. Theory Comput., 2013, 9 (7), pp 3084-3095. Application 67581468 resources: utime ~339s, stime ~1580s, Rss ~77924, inblocks ~1715814130, outblocks ~1045705536