CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/20/16 18:01:30 | Available memory: 3.102 GB INPUT: Reading input from 'pt-analysis.chi-py-py.in' [parm ../../aa/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apa]] Reading '../../aa/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../ag/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apg]] Reading '../../ag/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../ga/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpa]] Reading '../../ga/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../gg/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpg]] Reading '../../gg/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../ac/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apc]] Reading '../../ac/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../au/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apu]] Reading '../../au/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../gc/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpc]] Reading '../../gc/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../gu/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpu]] Reading '../../gu/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../ca/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpa]] Reading '../../ca/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../cg/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpg]] Reading '../../cg/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../ua/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upa]] Reading '../../ua/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../ug/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upg]] Reading '../../ug/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../cc/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpc]] Reading '../../cc/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../cu/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpu]] Reading '../../cu/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../uc/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upc]] Reading '../../uc/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../uu/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upu]] Reading '../../uu/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [trajin ../../cc/cluster-all/km-5/ctraj.c1 parm [cpc]] Reading '../../cc/cluster-all/km-5/ctraj.c1' as Amber NetCDF [trajin ../../cu/cluster-1-1/km-5-bbC2/ctraj.c1 parm [cpu]] Reading '../../cu/cluster-1-1/km-5-bbC2/ctraj.c1' as Amber NetCDF [trajin ../../uc/cluster-1-1/km-5/ctraj.c0 parm [upc]] Reading '../../uc/cluster-1-1/km-5/ctraj.c0' as Amber NetCDF [trajin ../../uu/cluster-all/km-5/ctraj.c0 parm [upu]] Reading '../../uu/cluster-all/km-5/ctraj.c0' as Amber NetCDF [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi out chi-1-py-py.dat] DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N1]-[:1@C2] Output range is -180 to 180 degrees. [dihedral c2 :2@O4' :2@C1' :2@N1 :2@C2 type chi out chi-2-py-py.dat] DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N1]-[:2@C2] Output range is -180 to 180 degrees. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (16 total): 0: [apa] noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol 1: [apg] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol 2: [gpa] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol 3: [gpg] noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol 4: [apc] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol 5: [apu] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol 6: [gpc] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol 7: [gpu] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol 8: [cpa] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol 9: [cpg] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol 10: [upa] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol 11: [upg] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol 12: [cpc] noWAt.topo.hmr, 61 atoms, 2 res, box: Orthogonal, 1 mol 13: [cpu] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol 14: [upc] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol 15: [upu] noWAt.topo.hmr, 59 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (4 total): 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 134387 of 134387) 1: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18571 of 18571) 2: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 36137 of 36137) 3: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 225909 of 225909) Coordinate processing will occur on 415004 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi out chi-1-py-py.dat] [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1) 1: [dihedral c2 :2@O4' :2@C1' :2@N1 :2@C2 type chi out chi-2-py-py.dat] [:2@O4'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1) ----- ctraj.c1 (1-134387, 1) ----- 0% 10% 20% 30% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi out chi-1-py-py.dat] [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1) 1: [dihedral c2 :2@O4' :2@C1' :2@N1 :2@C2 type chi out chi-2-py-py.dat] [:2@O4'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1) ----- ctraj.c1 (1-18571, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi out chi-1-py-py.dat] [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1) 1: [dihedral c2 :2@O4' :2@C1' :2@N1 :2@C2 type chi out chi-2-py-py.dat] [:2@O4'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1) ----- ctraj.c0 (1-36137, 1) ----- 40% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi out chi-1-py-py.dat] [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1) 1: [dihedral c2 :2@O4' :2@C1' :2@N1 :2@C2 type chi out chi-2-py-py.dat] [:2@O4'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1) ----- ctraj.c0 (1-225909, 1) ----- 50% 60% 70% 80% 90% 100% Complete. Read 415004 frames and processed 415004 frames. TIME: Avg. throughput= 466941.4281 frames / second. ACTION OUTPUT: DATASETS (2 total): c1 "c1" (double, torsion(chin)), size is 415004 c2 "c2" (double, torsion(chin)), size is 415004 DATAFILES (2 total): chi-1-py-py.dat (Standard Data File): c1 chi-2-py-py.dat (Standard Data File): c2 RUN TIMING: TIME: Init : 0.0004 s ( 0.02%) TIME: Trajectory Process : 0.8888 s ( 37.91%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 1.4555 s ( 62.08%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 2.3447 s ---------- RUN END --------------------------------------------------- [hist c1,-180,180,0.5 c2,-180,180,0.5 out 2dhist_c1_c2_yy.gnu norm] Hist: 2dhist_c1_c2_yy.gnu: Set up for 2 dimensions using the following datasets: [ c1 c2 ] norm: Sum over bins will be normalized to 1.0. ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (16 total): 0: [apa] noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol 1: [apg] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol 2: [gpa] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol 3: [gpg] noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol 4: [apc] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol 5: [apu] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol 6: [gpc] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol 7: [gpu] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol 8: [cpa] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol 9: [cpg] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol 10: [upa] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol 11: [upg] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol 12: [cpc] noWAt.topo.hmr, 61 atoms, 2 res, box: Orthogonal, 1 mol 13: [cpu] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol 14: [upc] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol 15: [upu] noWAt.topo.hmr, 59 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (4 total): 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 134387 of 134387) 1: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18571 of 18571) 2: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 36137 of 36137) 3: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 225909 of 225909) Coordinate processing will occur on 415004 frames. BEGIN TRAJECTORY PROCESSING: ----- ctraj.c1 (1-134387, 1) ----- 0% 10% 20% 30% ----- ctraj.c1 (1-18571, 1) ----- ----- ctraj.c0 (1-36137, 1) ----- 40% ----- ctraj.c0 (1-225909, 1) ----- 50% 60% 70% 80% 90% 100% Complete. Read 415004 frames and processed 415004 frames. TIME: Avg. throughput= 630517.3535 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [hist c1,-180,180,0.5 c2,-180,180,0.5 out 2dhist_c1_c2_yy.gnu norm] Calculating bins from min=-180 max=180 step=0.5. Dim c1: -180.000000->180.000000, step 0.500000, 720 bins. Calculating bins from min=-180 max=180 step=0.5. Dim c2: -180.000000->180.000000, step 0.500000, 720 bins. Hist: 415004 data points in each dimension. Hist: Allocating histogram, total bins = 518400 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 415004 TIME: Analyses took 0.0111 seconds. DATASETS (3 total): c1 "c1" (double, torsion(chin)), size is 415004 c2 "c2" (double, torsion(chin)), size is 415004 Hist_00018 "Hist_00018" (double matrix), size is 518400 DATAFILES (3 total): chi-1-py-py.dat (Standard Data File): c1 chi-2-py-py.dat (Standard Data File): c2 2dhist_c1_c2_yy.gnu (Gnuplot File): Hist_00018 RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 0.6582 s ( 44.35%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0111 s ( 0.75%) TIME: Data File Write : 0.8147 s ( 54.89%) TIME: Other : 0.0002 s ( 0.00%) TIME: Run Total 1.4842 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 3.8978 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.