CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 01/08/16 17:15:20 | Available memory: 60600.2 MB INPUT: Reading Input from file pt-diheds.in [parm ../../build/full.topo.hmr] Reading '../../build/full.topo.hmr' as Amber Topology CHAMBER topology: 1: CHARMM 361 * \\\\ CHARMM36 All-Hydrogen Nucleic Acid Topology File /// [strip :WAT,Na+,K+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,K+,Cl-] [autoimage origin] 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 Reading '../../traj.1.02' as Amber NetCDF Reading '../../traj.1.03' as Amber NetCDF Reading '../../traj.1.04' as Amber NetCDF Reading '../../traj.1.05' as Amber NetCDF Reading '../../traj.1.06' as Amber NetCDF Reading '../../traj.1.07' as Amber NetCDF Reading '../../traj.1.08' as Amber NetCDF Reading '../../traj.1.09' as Amber NetCDF Reading '../../traj.1.10' as Amber NetCDF Reading '../../traj.1.11' as Amber NetCDF Reading '../../traj.1.12' as Amber NetCDF Reading '../../traj.1.13' as Amber NetCDF Reading '../../traj.1.14' as Amber NetCDF Reading '../../traj.1.15' as Amber NetCDF Reading '../../traj.1.16' as Amber NetCDF Reading '../../traj.1.17' as Amber NetCDF Reading '../../traj.1.18' as Amber NetCDF [dihedral c1c4 :1@H1' :1@C1' :1@N9 :1@C4 out diheds.dat ] DIHEDRAL: [:1@H1']-[:1@C1']-[:1@N9]-[:1@C4] Output range is -180 to 180 degrees. [dihedral c1c8 :1@H1' :1@C1' :1@N9 :1@C8 out diheds.dat ] DIHEDRAL: [:1@H1']-[:1@C1']-[:1@N9]-[:1@C8] Output range is -180 to 180 degrees. [dihedral c2c4 :2@H1' :2@C1' :2@N1 :2@C2 out diheds.dat ] DIHEDRAL: [:2@H1']-[:2@C1']-[:2@N1]-[:2@C2] Output range is -180 to 180 degrees. [dihedral c2c8 :2@H1' :2@C1' :2@N1 :2@C6 out diheds.dat ] DIHEDRAL: [:2@H1']-[:2@C1']-[:2@N1]-[:2@C6] Output range is -180 to 180 degrees. [dihedral e1c4 :1@C4' :1@C3' :1@O3' :2@P out diheds.dat ] DIHEDRAL: [:1@C4']-[:1@C3']-[:1@O3']-[:2@P] Output range is -180 to 180 degrees. [dihedral e1c2 :1@C2' :1@C3' :1@O3' :2@P out diheds.dat ] DIHEDRAL: [:1@C2']-[:1@C3']-[:1@O3']-[:2@P] Output range is -180 to 180 degrees. [dihedral e1h3 :1@H3' :1@C3' :1@O3' :2@P out diheds.dat ] DIHEDRAL: [:1@H3']-[:1@C3']-[:1@O3']-[:2@P] Output range is -180 to 180 degrees. [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' out diheds.dat ] DIHEDRAL: [:2@P]-[:2@O5']-[:2@C5']-[:2@C4'] Output range is -180 to 180 degrees. [dihedral g1h4ph5p :1@H4' :1@C4' :1@C5' :1@H5' out diheds.dat ] DIHEDRAL: [:1@H4']-[:1@C4']-[:1@C5']-[:1@H5'] Output range is -180 to 180 degrees. [dihedral g2h4ph5p :2@H4' :2@C4' :2@C5' :2@H5' out diheds.dat ] DIHEDRAL: [:2@H4']-[:2@C4']-[:2@C5']-[:2@H5'] Output range is -180 to 180 degrees. [dihedral g1h4ph5s :1@H4' :1@C4' :1@C5' :1@H5'' out diheds.dat ] DIHEDRAL: [:1@H4']-[:1@C4']-[:1@C5']-[:1@H5''] Output range is -180 to 180 degrees. [dihedral g2h4ph5s :2@H4' :2@C4' :2@C5' :2@H5'' out diheds.dat ] DIHEDRAL: [:2@H4']-[:2@C4']-[:2@C5']-[:2@H5''] Output range is -180 to 180 degrees. [dihedral d1h3ph4p :1@H3' :1@C3' :1@C4' :1@H4' out diheds.dat ] DIHEDRAL: [:1@H3']-[:1@C3']-[:1@C4']-[:1@H4'] Output range is -180 to 180 degrees. [dihedral d2h3ph4p :2@H3' :2@C3' :2@C4' :2@H4' out diheds.dat ] DIHEDRAL: [:2@H3']-[:2@C3']-[:2@C4']-[:2@H4'] Output range is -180 to 180 degrees. ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: 'full.topo.hmr', 3299 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 50000 frames INPUT TRAJECTORIES: 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. TIME: Run Initialization took 0.0001 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM 'full.topo.hmr' (16 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 63 atoms, 2 res, box: Orthogonal, 1 mol 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [dihedral c1c4 :1@H1' :1@C1' :1@N9 :1@C4 out diheds.dat ] [:1@H1'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) 3: [dihedral c1c8 :1@H1' :1@C1' :1@N9 :1@C8 out diheds.dat ] [:1@H1'](1) [:1@C1'](1) [:1@N9](1) [:1@C8](1) 4: [dihedral c2c4 :2@H1' :2@C1' :2@N1 :2@C2 out diheds.dat ] [:2@H1'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1) 5: [dihedral c2c8 :2@H1' :2@C1' :2@N1 :2@C6 out diheds.dat ] [:2@H1'](1) [:2@C1'](1) [:2@N1](1) [:2@C6](1) 6: [dihedral e1c4 :1@C4' :1@C3' :1@O3' :2@P out diheds.dat ] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 7: [dihedral e1c2 :1@C2' :1@C3' :1@O3' :2@P out diheds.dat ] [:1@C2'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 8: [dihedral e1h3 :1@H3' :1@C3' :1@O3' :2@P out diheds.dat ] [:1@H3'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 9: [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' out diheds.dat ] [:2@P](1) [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) 10: [dihedral g1h4ph5p :1@H4' :1@C4' :1@C5' :1@H5' out diheds.dat ] [:1@H4'](1) [:1@C4'](1) [:1@C5'](1) [:1@H5'](1) 11: [dihedral g2h4ph5p :2@H4' :2@C4' :2@C5' :2@H5' out diheds.dat ] [:2@H4'](1) [:2@C4'](1) [:2@C5'](1) [:2@H5'](1) 12: [dihedral g1h4ph5s :1@H4' :1@C4' :1@C5' :1@H5'' out diheds.dat ] [:1@H4'](1) [:1@C4'](1) [:1@C5'](1) [:1@H5''](1) 13: [dihedral g2h4ph5s :2@H4' :2@C4' :2@C5' :2@H5'' out diheds.dat ] [:2@H4'](1) [:2@C4'](1) [:2@C5'](1) [:2@H5''](1) 14: [dihedral d1h3ph4p :1@H3' :1@C3' :1@C4' :1@H4' out diheds.dat ] [:1@H3'](1) [:1@C3'](1) [:1@C4'](1) [:1@H4'](1) 15: [dihedral d2h3ph4p :2@H3' :2@C3' :2@C4' :2@H4' out diheds.dat ] [:2@H3'](1) [:2@C3'](1) [:2@C4'](1) [:2@H4'](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: Trajectory processing: 1406.6501 s TIME: Avg. throughput= 35.5454 frames / second. ACTION OUTPUT: DATASETS: 14 data sets: c1c4 "c1c4" (double, torsion), size is 50000 c1c8 "c1c8" (double, torsion), size is 50000 c2c4 "c2c4" (double, torsion), size is 50000 c2c8 "c2c8" (double, torsion), size is 50000 e1c4 "e1c4" (double, torsion), size is 50000 e1c2 "e1c2" (double, torsion), size is 50000 e1h3 "e1h3" (double, torsion), size is 50000 b2 "b2" (double, torsion), size is 50000 g1h4ph5p "g1h4ph5p" (double, torsion), size is 50000 g2h4ph5p "g2h4ph5p" (double, torsion), size is 50000 g1h4ph5s "g1h4ph5s" (double, torsion), size is 50000 g2h4ph5s "g2h4ph5s" (double, torsion), size is 50000 d1h3ph4p "d1h3ph4p" (double, torsion), size is 50000 d2h3ph4p "d2h3ph4p" (double, torsion), size is 50000 DATAFILES: diheds.dat (Standard Data File): c1c4 c1c8 c2c4 c2c8 ... g1h4ph5s g2h4ph5s d1h3ph4p d2h3ph4p ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1410.9110 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.