CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 03/23/16 08:16:24 | Available memory: 16.232 GB INPUT: Reading input from 'pt-test.in' [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [autoimage origin] Warning: Action specified before trajin/ensemble. Assuming trajin. AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [trajin ../../traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18] Reading '../../traj.1.01' as Amber NetCDF [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma] DIHEDRAL: [:1@O5']-[:1@C5']-[:1@C4']-[:1@C3'] 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 c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi] DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N1]-[:1@C2] 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. [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta] DIHEDRAL: [:2@P]-[:2@O5']-[:2@C5']-[:2@C4'] Output range is -180 to 180 degrees. [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma] DIHEDRAL: [:2@O5']-[:2@C5']-[:2@C4']-[:2@C3'] Output range is -180 to 180 degrees. [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] DIHEDRAL: [:2@C5']-[:2@C4']-[:2@C3']-[:2@O3'] Output range is -180 to 180 degrees. [dihedral c2 :2@O4' :2@C1' :2@N1 :2@C2 type chi] DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N1]-[:2@C2] Output range is -180 to 180 degrees. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: [traj] full.topo.hmr, 3319 atoms, 1088 res, box: Orthogonal, 1087 mol, 1085 solvent INPUT TRAJECTORIES (1 total): 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K Coordinate processing will occur on 50000 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'full.topo.hmr' (12 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 2: [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma] [:1@O5'](1) [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) 3: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 4: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 5: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 6: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1) 7: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) 8: [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta] [:2@P](1) [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) 9: [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma] [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) 10: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 11: [dihedral c2 :2@O4' :2@C1' :2@N1 :2@C2 type chi] [:2@O4'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1) ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Avg. throughput= 81.7550 frames / second. ACTION OUTPUT: DATASETS (10 total): g1 "g1" (double, torsion(gamma)), size is 50000 d1 "d1" (double, torsion(delta)), size is 50000 e1 "e1" (double, torsion(epsilon)), size is 50000 z1 "z1" (double, torsion(zeta)), size is 50000 c1 "c1" (double, torsion(chin)), size is 50000 a2 "a2" (double, torsion(alpha)), size is 50000 b2 "b2" (double, torsion(beta)), size is 50000 g2 "g2" (double, torsion(gamma)), size is 50000 d2 "d2" (double, torsion(delta)), size is 50000 c2 "c2" (double, torsion(chin)), size is 50000 RUN TIMING: TIME: Init : 0.0001 s ( 0.00%) TIME: Trajectory Process : 611.5835 s (100.00%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.0167 s ( 0.00%) TIME: Other : 0.0003 s ( 0.00%) TIME: Run Total 611.6005 s ---------- RUN END --------------------------------------------------- [hist g1,-180,180,1 out dihed_g1-hist_Run1.dat norm] Hist: dihed_g1-hist_Run1.dat: Set up for 1 dimensions using the following datasets: [ g1 ] norm: Sum over bins will be normalized to 1.0. [hist d1,-180,180,1 out dihed_d1-hist_Run1.dat norm] Hist: dihed_d1-hist_Run1.dat: Set up for 1 dimensions using the following datasets: [ d1 ] norm: Sum over bins will be normalized to 1.0. [hist e1,-180,180,1 out dihed_e1-hist_Run1.dat norm] Hist: dihed_e1-hist_Run1.dat: Set up for 1 dimensions using the following datasets: [ e1 ] norm: Sum over bins will be normalized to 1.0. [hist z1,-180,180,1 out dihed_z1-hist_Run1.dat norm] Hist: dihed_z1-hist_Run1.dat: Set up for 1 dimensions using the following datasets: [ z1 ] norm: Sum over bins will be normalized to 1.0. [hist c1,-180,180,1 out dihed_c1-hist_Run1.dat norm] Hist: dihed_c1-hist_Run1.dat: Set up for 1 dimensions using the following datasets: [ c1 ] norm: Sum over bins will be normalized to 1.0. [hist a2,-180,180,1 out dihed_a2-hist_Run1.dat norm] Hist: dihed_a2-hist_Run1.dat: Set up for 1 dimensions using the following datasets: [ a2 ] norm: Sum over bins will be normalized to 1.0. [hist b2,-180,180,1 out dihed_b2-hist_Run1.dat norm] Hist: dihed_b2-hist_Run1.dat: Set up for 1 dimensions using the following datasets: [ b2 ] norm: Sum over bins will be normalized to 1.0. [hist g2,-180,180,1 out dihed_g2-hist_Run1.dat norm] Hist: dihed_g2-hist_Run1.dat: Set up for 1 dimensions using the following datasets: [ g2 ] norm: Sum over bins will be normalized to 1.0. [hist d2,-180,180,1 out dihed_d2-hist_Run1.dat norm] Hist: dihed_d2-hist_Run1.dat: Set up for 1 dimensions using the following datasets: [ d2 ] norm: Sum over bins will be normalized to 1.0. [hist c2,-180,180,1 out dihed_c2-hist_Run1.dat norm] Hist: dihed_c2-hist_Run1.dat: Set up for 1 dimensions using the following datasets: [ c2 ] norm: Sum over bins will be normalized to 1.0. ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: [traj] full.topo.hmr, 3319 atoms, 1088 res, box: Orthogonal, 1087 mol, 1085 solvent INPUT TRAJECTORIES (1 total): 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K Coordinate processing will occur on 50000 frames. BEGIN TRAJECTORY PROCESSING: ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Avg. throughput= 80.5933 frames / second. ACTION OUTPUT: ANALYSIS: Performing 10 analyses: 0: [hist g1,-180,180,1 out dihed_g1-hist_Run1.dat norm] Calculating bins from min=-180 max=180 step=1. Dim g1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 50000 1: [hist d1,-180,180,1 out dihed_d1-hist_Run1.dat norm] Calculating bins from min=-180 max=180 step=1. Dim d1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 50000 2: [hist e1,-180,180,1 out dihed_e1-hist_Run1.dat norm] Calculating bins from min=-180 max=180 step=1. Dim e1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 50000 3: [hist z1,-180,180,1 out dihed_z1-hist_Run1.dat norm] Calculating bins from min=-180 max=180 step=1. Dim z1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 50000 4: [hist c1,-180,180,1 out dihed_c1-hist_Run1.dat norm] Calculating bins from min=-180 max=180 step=1. Dim c1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 50000 5: [hist a2,-180,180,1 out dihed_a2-hist_Run1.dat norm] Calculating bins from min=-180 max=180 step=1. Dim a2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 50000 6: [hist b2,-180,180,1 out dihed_b2-hist_Run1.dat norm] Calculating bins from min=-180 max=180 step=1. Dim b2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 50000 7: [hist g2,-180,180,1 out dihed_g2-hist_Run1.dat norm] Calculating bins from min=-180 max=180 step=1. Dim g2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 50000 8: [hist d2,-180,180,1 out dihed_d2-hist_Run1.dat norm] Calculating bins from min=-180 max=180 step=1. Dim d2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 50000 9: [hist c2,-180,180,1 out dihed_c2-hist_Run1.dat norm] Calculating bins from min=-180 max=180 step=1. Dim c2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 360 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 50000 TIME: Analyses took 0.2104 seconds. DATASETS (20 total): g1 "g1" (double, torsion(gamma)), size is 50000 d1 "d1" (double, torsion(delta)), size is 50000 e1 "e1" (double, torsion(epsilon)), size is 50000 z1 "z1" (double, torsion(zeta)), size is 50000 c1 "c1" (double, torsion(chin)), size is 50000 a2 "a2" (double, torsion(alpha)), size is 50000 b2 "b2" (double, torsion(beta)), size is 50000 g2 "g2" (double, torsion(gamma)), size is 50000 d2 "d2" (double, torsion(delta)), size is 50000 c2 "c2" (double, torsion(chin)), size is 50000 Hist_00011 "Hist_00011" (double), size is 360 Hist_00012 "Hist_00012" (double), size is 360 Hist_00013 "Hist_00013" (double), size is 360 Hist_00014 "Hist_00014" (double), size is 360 Hist_00015 "Hist_00015" (double), size is 360 Hist_00016 "Hist_00016" (double), size is 360 Hist_00017 "Hist_00017" (double), size is 360 Hist_00018 "Hist_00018" (double), size is 360 Hist_00019 "Hist_00019" (double), size is 360 Hist_00020 "Hist_00020" (double), size is 360 DATAFILES (10 total): dihed_g1-hist_Run1.dat (Standard Data File): Hist_00011 dihed_d1-hist_Run1.dat (Standard Data File): Hist_00012 dihed_e1-hist_Run1.dat (Standard Data File): Hist_00013 dihed_z1-hist_Run1.dat (Standard Data File): Hist_00014 dihed_c1-hist_Run1.dat (Standard Data File): Hist_00015 dihed_a2-hist_Run1.dat (Standard Data File): Hist_00016 dihed_b2-hist_Run1.dat (Standard Data File): Hist_00017 dihed_g2-hist_Run1.dat (Standard Data File): Hist_00018 dihed_d2-hist_Run1.dat (Standard Data File): Hist_00019 dihed_c2-hist_Run1.dat (Standard Data File): Hist_00020 RUN TIMING: TIME: Init : 0.0001 s ( 0.00%) TIME: Trajectory Process : 620.3989 s ( 99.72%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.2104 s ( 0.03%) TIME: Data File Write : 1.5063 s ( 0.24%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 622.1158 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1235.5787 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.