CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/25/16 12:13:43 | Available memory: 1.744 GB INPUT: Reading input from 'pt-analysis2.in' [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr] Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [trajin ../ctraj.c1] Reading '../ctraj.c1' as Amber NetCDF [reference ../../../A-form.pdb [a-form]] Reading '../../../A-form.pdb' as PDB Setting active reference for distance-based masks: 'A-form.pdb' [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass] RMSD: (:1,2&!@H*), reference is "[a-form]:1" (:1,2&!@H*), mass-weighted. Best-fit RMSD will be calculated, coords will be rotated and translated. [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@N9 :1@C4 type chi] DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N9]-[:1@C4] 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@N9 :2@C4 type chi] DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N9]-[:2@C4] Output range is -180 to 180 degrees. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 164404 of 164404) Coordinate processing will occur on 164404 frames. REFERENCE FRAMES (1 total): 0: [a-form]:1 Active reference frame for distance-based masks is '[a-form]:1' BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (11 actions): 0: [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass] Target mask: [:1,2&!@H*](41) Reference mask: [:1,2&!@H*](41) 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. 1: [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma] [:1@O5'](1) [:1@C5'](1) [:1@C4'](1) [:1@C3'](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 c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) 6: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) 7: [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta] [:2@P](1) [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) 8: [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma] [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) 9: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 10: [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chi] [:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1) ----- ctraj.c1 (1-164404, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 164404 frames and processed 164404 frames. TIME: Avg. throughput= 86078.3220 frames / second. ACTION OUTPUT: DATASETS (11 total): rms_2_aform "rms_2_aform" (double, rms), size is 164404 g1 "g1" (double, torsion(gamma)), size is 164404 d1 "d1" (double, torsion(delta)), size is 164404 e1 "e1" (double, torsion(epsilon)), size is 164404 z1 "z1" (double, torsion(zeta)), size is 164404 c1 "c1" (double, torsion(chin)), size is 164404 a2 "a2" (double, torsion(alpha)), size is 164404 b2 "b2" (double, torsion(beta)), size is 164404 g2 "g2" (double, torsion(gamma)), size is 164404 d2 "d2" (double, torsion(delta)), size is 164404 c2 "c2" (double, torsion(chin)), size is 164404 RUN TIMING: TIME: Init : 0.0001 s ( 0.00%) TIME: Trajectory Process : 1.9099 s ( 99.99%) 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 1.9101 s ---------- RUN END --------------------------------------------------- [hist z1,-180,180,1 a2,-180,180,1 out 2dhist_z1_a2.gnu norm] Hist: 2dhist_z1_a2.gnu: Set up for 2 dimensions using the following datasets: [ z1 a2 ] norm: Sum over bins will be normalized to 1.0. [hist z1,-180,180,1 c1,-180,180,1 out 2dhist_z1_c1.gnu norm] Hist: 2dhist_z1_c1.gnu: Set up for 2 dimensions using the following datasets: [ z1 c1 ] norm: Sum over bins will be normalized to 1.0. ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 164404 of 164404) Coordinate processing will occur on 164404 frames. REFERENCE FRAMES (1 total): 0: [a-form]:1 Active reference frame for distance-based masks is '[a-form]:1' BEGIN TRAJECTORY PROCESSING: ----- ctraj.c1 (1-164404, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 164404 frames and processed 164404 frames. TIME: Avg. throughput= 894238.7189 frames / second. ACTION OUTPUT: ANALYSIS: Performing 2 analyses: 0: [hist z1,-180,180,1 a2,-180,180,1 out 2dhist_z1_a2.gnu norm] Calculating bins from min=-180 max=180 step=1. Dim z1: -180.000000->180.000000, step 1.000000, 360 bins. Calculating bins from min=-180 max=180 step=1. Dim a2: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 164404 data points in each dimension. Hist: Allocating histogram, total bins = 129600 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 164404 1: [hist z1,-180,180,1 c1,-180,180,1 out 2dhist_z1_c1.gnu norm] Calculating bins from min=-180 max=180 step=1. Dim z1: -180.000000->180.000000, step 1.000000, 360 bins. Calculating bins from min=-180 max=180 step=1. Dim c1: -180.000000->180.000000, step 1.000000, 360 bins. Hist: 164404 data points in each dimension. Hist: Allocating histogram, total bins = 129600 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 164404 TIME: Analyses took 0.0077 seconds. DATASETS (13 total): rms_2_aform "rms_2_aform" (double, rms), size is 164404 g1 "g1" (double, torsion(gamma)), size is 164404 d1 "d1" (double, torsion(delta)), size is 164404 e1 "e1" (double, torsion(epsilon)), size is 164404 z1 "z1" (double, torsion(zeta)), size is 164404 c1 "c1" (double, torsion(chin)), size is 164404 a2 "a2" (double, torsion(alpha)), size is 164404 b2 "b2" (double, torsion(beta)), size is 164404 g2 "g2" (double, torsion(gamma)), size is 164404 d2 "d2" (double, torsion(delta)), size is 164404 c2 "c2" (double, torsion(chin)), size is 164404 Hist_00013 "Hist_00013" (double matrix), size is 129600 Hist_00014 "Hist_00014" (double matrix), size is 129600 DATAFILES (2 total): 2dhist_z1_a2.gnu (Gnuplot File): Hist_00013 2dhist_z1_c1.gnu (Gnuplot File): Hist_00014 RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 0.1838 s ( 24.97%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0077 s ( 1.05%) TIME: Data File Write : 0.5447 s ( 73.98%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.7363 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 2.7351 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.