CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/21/16 12:26:10 | Available memory: 3.518 GB INPUT: Reading input from 'pt-analysis.chi-pu-pu.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 ../../aa/cluster-all/km-7/ctraj.c3 parm [apa]] Reading '../../aa/cluster-all/km-7/ctraj.c3' as Amber NetCDF [trajin ../../ag/cluster-all/km-6/ctraj.c3 parm [apg]] Reading '../../ag/cluster-all/km-6/ctraj.c3' as Amber NetCDF [trajin ../../ag/cluster-all/km-6/ctraj.c4 parm [apg]] Reading '../../ag/cluster-all/km-6/ctraj.c4' as Amber NetCDF [trajin ../../ga/cluster-1-1/km-5/ctraj.c3 parm [gpa]] Reading '../../ga/cluster-1-1/km-5/ctraj.c3' as Amber NetCDF [trajin ../../gg/cluster-all/km-6/ctraj.c3 parm [gpg]] Reading '../../gg/cluster-all/km-6/ctraj.c3' as Amber NetCDF [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N9]-[:1@C4] Output range is -180 to 180 degrees. [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi] DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N9]-[:2@C4] Output range is -180 to 180 degrees. [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] DIHEDRAL: [:1@C5']-[:1@C4']-[:1@C3']-[:1@O3'] Output range is -180 to 180 degrees. [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] DIHEDRAL: [:1@C4']-[:1@C3']-[:1@O3']-[:2@P] Output range is -180 to 180 degrees. [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] DIHEDRAL: [:1@C3']-[:1@O3']-[:2@P]-[:2@O5'] Output range is -180 to 180 degrees. [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] DIHEDRAL: [:1@O3']-[:2@P]-[:2@O5']-[:2@C5'] 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 (5 total): 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 50960 of 50960) 1: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 71210 of 71210) 2: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 47954 of 47954) 3: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7174 of 7174) 4: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 47410 of 47410) Coordinate processing will occur on 224708 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) 1: [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi] [:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1) 2: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c3 (1-50960, 1) ----- 0% 10% 20% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) 1: [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi] [:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1) 2: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c3 (1-71210, 1) ----- 30% 40% 50% ----- ctraj.c4 (1-47954, 1) ----- 60% 70% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) 1: [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi] [:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1) 2: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c3 (1-7174, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) 1: [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi] [:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1) 2: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c3 (1-47410, 1) ----- 80% 90% 100% Complete. Read 224708 frames and processed 224708 frames. TIME: Avg. throughput= 286079.8525 frames / second. ACTION OUTPUT: DATASETS (6 total): c1 "c1" (double, torsion(chin)), size is 224708 c2 "c2" (double, torsion(chin)), size is 224708 d1 "d1" (double, torsion(delta)), size is 224708 e1 "e1" (double, torsion(epsilon)), size is 224708 z1 "z1" (double, torsion(zeta)), size is 224708 a2 "a2" (double, torsion(alpha)), size is 224708 RUN TIMING: TIME: Init : 0.0001 s ( 0.01%) TIME: Trajectory Process : 0.7855 s ( 99.98%) 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 : 0.0000 s ( 0.00%) TIME: Run Total 0.7856 s ---------- RUN END --------------------------------------------------- [hist c1,-180,180,0.5 c2,-180,180,0.5 out 2dhist_c1_c2_uu.gnu norm] Hist: 2dhist_c1_c2_uu.gnu: Set up for 2 dimensions using the following datasets: [ c1 c2 ] norm: Sum over bins will be normalized to 1.0. [hist d1,-180,180,0.5 c2,-180,180,0.5 out 2dhist_d1_c2_uu.gnu norm] Hist: 2dhist_d1_c2_uu.gnu: Set up for 2 dimensions using the following datasets: [ d1 c2 ] norm: Sum over bins will be normalized to 1.0. [hist z1,-180,180,0.5 c2,-180,180,0.5 out 2dhist_z1_c2_uu.gnu norm] Hist: 2dhist_z1_c2_uu.gnu: Set up for 2 dimensions using the following datasets: [ z1 c2 ] norm: Sum over bins will be normalized to 1.0. [hist a2,-180,180,0.5 c2,-180,180,0.5 out 2dhist_a2_c2_uu.gnu norm] Hist: 2dhist_a2_c2_uu.gnu: Set up for 2 dimensions using the following datasets: [ a2 c2 ] norm: Sum over bins will be normalized to 1.0. [hist z1,-180,180,0.5 a2,-180,180,0.5 out 2dhist_z1_a2_uu.gnu norm] Hist: 2dhist_z1_a2_uu.gnu: Set up for 2 dimensions using the following datasets: [ z1 a2 ] 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 (5 total): 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 50960 of 50960) 1: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 71210 of 71210) 2: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 47954 of 47954) 3: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7174 of 7174) 4: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 47410 of 47410) Coordinate processing will occur on 224708 frames. BEGIN TRAJECTORY PROCESSING: ----- ctraj.c3 (1-50960, 1) ----- 0% 10% 20% ----- ctraj.c3 (1-71210, 1) ----- 30% 40% 50% ----- ctraj.c4 (1-47954, 1) ----- 60% 70% ----- ctraj.c3 (1-7174, 1) ----- ----- ctraj.c3 (1-47410, 1) ----- 80% 90% 100% Complete. Read 224708 frames and processed 224708 frames. TIME: Avg. throughput= 522401.8003 frames / second. ACTION OUTPUT: ANALYSIS: Performing 5 analyses: 0: [hist c1,-180,180,0.5 c2,-180,180,0.5 out 2dhist_c1_c2_uu.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: 224708 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 224708 1: [hist d1,-180,180,0.5 c2,-180,180,0.5 out 2dhist_d1_c2_uu.gnu norm] Calculating bins from min=-180 max=180 step=0.5. Dim d1: -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: 224708 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 224708 2: [hist z1,-180,180,0.5 c2,-180,180,0.5 out 2dhist_z1_c2_uu.gnu norm] Calculating bins from min=-180 max=180 step=0.5. Dim z1: -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: 224708 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 224708 3: [hist a2,-180,180,0.5 c2,-180,180,0.5 out 2dhist_a2_c2_uu.gnu norm] Calculating bins from min=-180 max=180 step=0.5. Dim a2: -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: 224708 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 224708 4: [hist z1,-180,180,0.5 a2,-180,180,0.5 out 2dhist_z1_a2_uu.gnu norm] Calculating bins from min=-180 max=180 step=0.5. Dim z1: -180.000000->180.000000, step 0.500000, 720 bins. Calculating bins from min=-180 max=180 step=0.5. Dim a2: -180.000000->180.000000, step 0.500000, 720 bins. Hist: 224708 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 224708 TIME: Analyses took 0.0614 seconds. DATASETS (11 total): c1 "c1" (double, torsion(chin)), size is 224708 c2 "c2" (double, torsion(chin)), size is 224708 d1 "d1" (double, torsion(delta)), size is 224708 e1 "e1" (double, torsion(epsilon)), size is 224708 z1 "z1" (double, torsion(zeta)), size is 224708 a2 "a2" (double, torsion(alpha)), size is 224708 Hist_00022 "Hist_00022" (double matrix), size is 518400 Hist_00023 "Hist_00023" (double matrix), size is 518400 Hist_00024 "Hist_00024" (double matrix), size is 518400 Hist_00025 "Hist_00025" (double matrix), size is 518400 Hist_00026 "Hist_00026" (double matrix), size is 518400 DATAFILES (5 total): 2dhist_c1_c2_uu.gnu (Gnuplot File): Hist_00022 2dhist_d1_c2_uu.gnu (Gnuplot File): Hist_00023 2dhist_z1_c2_uu.gnu (Gnuplot File): Hist_00024 2dhist_a2_c2_uu.gnu (Gnuplot File): Hist_00025 2dhist_z1_a2_uu.gnu (Gnuplot File): Hist_00026 RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 0.4301 s ( 8.41%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0614 s ( 1.20%) TIME: Data File Write : 4.6234 s ( 90.38%) TIME: Other : 0.0007 s ( 0.00%) TIME: Run Total 5.1157 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 5.9720 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.