CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 01/08/16 17:15:21 | Available memory: 53722.9 MB INPUT: Reading Input from file pt-diheds.in [parm ../../build/full.topo.hmr] Reading '../../build/full.topo.hmr' as Amber Topology [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', 4374 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 49733 frames INPUT TRAJECTORIES: 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 49733 of 49733) Looking for frames at 298.41 K Coordinate processing will occur on 49733 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 4311 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 (1-49733, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 49733 frames and processed 49733 frames. TIME: Trajectory processing: 1477.3125 s TIME: Avg. throughput= 33.6645 frames / second. ACTION OUTPUT: DATASETS: 14 data sets: c1c4 "c1c4" (double, torsion), size is 49733 c1c8 "c1c8" (double, torsion), size is 49733 c2c4 "c2c4" (double, torsion), size is 49733 c2c8 "c2c8" (double, torsion), size is 49733 e1c4 "e1c4" (double, torsion), size is 49733 e1c2 "e1c2" (double, torsion), size is 49733 e1h3 "e1h3" (double, torsion), size is 49733 b2 "b2" (double, torsion), size is 49733 g1h4ph5p "g1h4ph5p" (double, torsion), size is 49733 g2h4ph5p "g2h4ph5p" (double, torsion), size is 49733 g1h4ph5s "g1h4ph5s" (double, torsion), size is 49733 g2h4ph5s "g2h4ph5s" (double, torsion), size is 49733 d1h3ph4p "d1h3ph4p" (double, torsion), size is 49733 d2h3ph4p "d2h3ph4p" (double, torsion), size is 49733 DATAFILES: diheds.dat (Standard Data File): c1c4 c1c8 c2c4 c2c8 ... g1h4ph5s g2h4ph5s d1h3ph4p d2h3ph4p ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1483.2959 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.