CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/13/15 01:43:25 | Available memory: 86894.7 MB INPUT: Reading Input from file pt-hb-rna.in [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [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,] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [hbond :1-2 avgout avghb-rna.dat printatomnum] HBOND: Searching for Hbond donors/acceptors in region specified by :1-2 Distance cutoff = 3.000, Angle Cutoff = 135.000 Writing Hbond avgs to avghb-rna.dat Atom numbers will be written to output. ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3295 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 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[traj]' (3 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 2: [hbond :1-2 avgout avghb-rna.dat printatomnum] Set up 18 acceptors: Set up 6 donors: Imaging off. Estimated max potential memory usage: 0.01 MB ----- 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: 39.7186 s TIME: Avg. throughput= 1258.8550 frames / second. ACTION OUTPUT: HBOND: Actual memory usage is 0.00 MB 34 solute-solute hydrogen bonds. DATASETS: 1 data set: HB_00000[UU] "HB_00000[UU]" (integer), size is 50000 DATAFILES: avghb-rna.dat (Avg. solute-solute HBonds) ---------- RUN END --------------------------------------------------- TIME: Total execution time: 40.5543 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.