CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/11/15 11:34:31 | Available memory: 28172.8 MB INPUT: Reading Input from file pt-randomize.in [parm full.topo] Reading 'full.topo' as Amber Topology [trajin non-randomized.crds] Reading 'non-randomized.crds' as Amber Restart [trajout rand.crds restart] Writing 'rand.crds' as Amber Restart [randomizeions :3 around :1-2 by 4.0 overlap 4.0 noimage seed 3] RANDOMIZEIONS: swapping the postions of the ions in mask [:3] with the solvent. No ions can get closer than 4.00 angstroms to another ion. No ion can get closer than 4.00 angstroms to mask [:1-2] Imaging of the coordinates will not be performed. Random number generator seed is 3 ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: 'full.topo', 3321 atoms, 1088 res, box: Orthogonal, 1087 mol, 1085 solvent, 1 frames INPUT TRAJECTORIES: 0: 'non-randomized.crds' is an AMBER restart file, no velocities, Parm full.topo (Orthogonal box) (reading 1 of 1) Coordinate processing will occur on 1 frames. OUTPUT TRAJECTORIES: 'rand.crds' is an AMBER restart file, Parm full.topo: Writing 1 frames (1-Last, 1) TIME: Run Initialization took 0.0127 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'full.topo' (1 actions): 0: [randomizeions :3 around :1-2 by 4.0 overlap 4.0 noimage seed 3] Ion mask is [:3] (1 atoms) Around mask is [:1-2] (65 atoms) ----- non-randomized.crds (1-1, 1) ----- 100% Complete. Read 1 frames and processed 1 frames. TIME: Trajectory processing: 0.0130 s TIME: Avg. throughput= 76.7519 frames / second. ACTION OUTPUT: ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.5207 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.