CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/01/16 10:57:27 | Available memory: 63841.8 MB INPUT: Reading Input from file pt-test.in [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [parm ../../../../../A-form.pdb [striped]] Reading '../../../../../A-form.pdb' as PDB File A-form.pdb: determining bond info from distances. Warning: A-form.pdb: Determining default bond distances from element types. [reference ../../../../../A-form.pdb parm [striped] [a-form]] Reading '../../../../../A-form.pdb' as PDB [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. [rmsd rms_2_aform :1,2&!@H= ref [a-form] ] Reference mask: [:1,2&!@H*](41) RMSD: (:1,2&!@H*), reference is "A-form.pdb" (:1,2&!@H*), with fitting. [distance dist_O2'-O4' :1@O2' :2@O4' ] DISTANCE: :1@O2' to :2@O4', center of mass. [distance 2pOP1 :1@HO2' :2@OP1] DISTANCE: :1@HO2' to :2@OP1, center of mass. [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. [ensemble ../../traj.1.01 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,] [run] ---------- RUN BEGIN ------------------------------------------------- INPUT ENSEMBLE: Ensemble size is 18 Ensemble Temperature Map: 280.00 -> 0 286.04 -> 1 292.18 -> 2 298.41 -> 3 304.74 -> 4 311.17 -> 5 317.69 -> 6 324.31 -> 7 331.03 -> 8 337.85 -> 9 344.79 -> 10 351.82 -> 11 358.97 -> 12 366.22 -> 13 373.59 -> 14 381.07 -> 15 388.67 -> 16 396.40 -> 17 INPUT TRAJECTORIES: 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Processing ensemble using replica temperatures Coordinate processing will occur on 50000 frames. PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 50000 frames 1: [striped] 'A-form.pdb', 65 atoms, 2 res, box: None, 1 mol REFERENCE FRAMES (1 total): 0: '../../../../../A-form.pdb', frame 1 Active reference frame for distance-based masks is 0 ENSEMBLE OUTPUT TRAJECTORIES (Numerical filename suffix corresponds to above map): TIME: Run Initialization took 0.0339 seconds. BEGIN ENSEMBLE PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES Warning: Active reference has only 65 atoms, parm '[traj]' has 3301. Warning: Parm will only have reference coordinates for the first 65 atoms (distance-based masks only). ..................................................... ACTION SETUP FOR PARM '[traj]' (6 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [rmsd rms_2_aform :1,2&!@H= ref [a-form] ] Target 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. 3: [distance dist_O2'-O4' :1@O2' :2@O4' ] :1@O2' (1 atoms) to :2@O4' (1 atoms), imaged. 4: [distance 2pOP1 :1@HO2' :2@OP1] :1@HO2' (1 atoms) to :2@OP1 (1 atoms), imaged. 5: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](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: 888.9856 s TIME: Avg. throughput= 56.2439 frames / second. ENSEMBLE ACTION OUTPUT: DATASETS: 73 data sets: [a-form]:1%0 "[a-form]:1" (reference), size is 1 '../../../../../A-form.pdb', refindex 0 (65 atoms) rms_2_aform%0 "rms_2_aform" (double, rms), size is 50000 dist_O2'-O4'%0 "dist_O2'-O4'" (double, distance), size is 50000 2pOP1%0 "2pOP1" (double, distance), size is 50000 z1%0 "z1" (double, torsion(zeta)), size is 50000 rms_2_aform%1 "rms_2_aform%1" (double, rms), size is 50000 dist_O2'-O4'%1 "dist_O2'-O4'%1" (double, distance), size is 50000 2pOP1%1 "2pOP1%1" (double, distance), size is 50000 z1%1 "z1%1" (double, torsion(zeta)), size is 50000 rms_2_aform%2 "rms_2_aform%2" (double, rms), size is 50000 dist_O2'-O4'%2 "dist_O2'-O4'%2" (double, distance), size is 50000 2pOP1%2 "2pOP1%2" (double, distance), size is 50000 z1%2 "z1%2" (double, torsion(zeta)), size is 50000 rms_2_aform%3 "rms_2_aform%3" (double, rms), size is 50000 dist_O2'-O4'%3 "dist_O2'-O4'%3" (double, distance), size is 50000 2pOP1%3 "2pOP1%3" (double, distance), size is 50000 z1%3 "z1%3" (double, torsion(zeta)), size is 50000 rms_2_aform%4 "rms_2_aform%4" (double, rms), size is 50000 dist_O2'-O4'%4 "dist_O2'-O4'%4" (double, distance), size is 50000 2pOP1%4 "2pOP1%4" (double, distance), size is 50000 z1%4 "z1%4" (double, torsion(zeta)), size is 50000 rms_2_aform%5 "rms_2_aform%5" (double, rms), size is 50000 dist_O2'-O4'%5 "dist_O2'-O4'%5" (double, distance), size is 50000 2pOP1%5 "2pOP1%5" (double, distance), size is 50000 z1%5 "z1%5" (double, torsion(zeta)), size is 50000 rms_2_aform%6 "rms_2_aform%6" (double, rms), size is 50000 dist_O2'-O4'%6 "dist_O2'-O4'%6" (double, distance), size is 50000 2pOP1%6 "2pOP1%6" (double, distance), size is 50000 z1%6 "z1%6" (double, torsion(zeta)), size is 50000 rms_2_aform%7 "rms_2_aform%7" (double, rms), size is 50000 dist_O2'-O4'%7 "dist_O2'-O4'%7" (double, distance), size is 50000 2pOP1%7 "2pOP1%7" (double, distance), size is 50000 z1%7 "z1%7" (double, torsion(zeta)), size is 50000 rms_2_aform%8 "rms_2_aform%8" (double, rms), size is 50000 dist_O2'-O4'%8 "dist_O2'-O4'%8" (double, distance), size is 50000 2pOP1%8 "2pOP1%8" (double, distance), size is 50000 z1%8 "z1%8" (double, torsion(zeta)), size is 50000 rms_2_aform%9 "rms_2_aform%9" (double, rms), size is 50000 dist_O2'-O4'%9 "dist_O2'-O4'%9" (double, distance), size is 50000 2pOP1%9 "2pOP1%9" (double, distance), size is 50000 z1%9 "z1%9" (double, torsion(zeta)), size is 50000 rms_2_aform%10 "rms_2_aform%10" (double, rms), size is 50000 dist_O2'-O4'%10 "dist_O2'-O4'%10" (double, distance), size is 50000 2pOP1%10 "2pOP1%10" (double, distance), size is 50000 z1%10 "z1%10" (double, torsion(zeta)), size is 50000 rms_2_aform%11 "rms_2_aform%11" (double, rms), size is 50000 dist_O2'-O4'%11 "dist_O2'-O4'%11" (double, distance), size is 50000 2pOP1%11 "2pOP1%11" (double, distance), size is 50000 z1%11 "z1%11" (double, torsion(zeta)), size is 50000 rms_2_aform%12 "rms_2_aform%12" (double, rms), size is 50000 dist_O2'-O4'%12 "dist_O2'-O4'%12" (double, distance), size is 50000 2pOP1%12 "2pOP1%12" (double, distance), size is 50000 z1%12 "z1%12" (double, torsion(zeta)), size is 50000 rms_2_aform%13 "rms_2_aform%13" (double, rms), size is 50000 dist_O2'-O4'%13 "dist_O2'-O4'%13" (double, distance), size is 50000 2pOP1%13 "2pOP1%13" (double, distance), size is 50000 z1%13 "z1%13" (double, torsion(zeta)), size is 50000 rms_2_aform%14 "rms_2_aform%14" (double, rms), size is 50000 dist_O2'-O4'%14 "dist_O2'-O4'%14" (double, distance), size is 50000 2pOP1%14 "2pOP1%14" (double, distance), size is 50000 z1%14 "z1%14" (double, torsion(zeta)), size is 50000 rms_2_aform%15 "rms_2_aform%15" (double, rms), size is 50000 dist_O2'-O4'%15 "dist_O2'-O4'%15" (double, distance), size is 50000 2pOP1%15 "2pOP1%15" (double, distance), size is 50000 z1%15 "z1%15" (double, torsion(zeta)), size is 50000 rms_2_aform%16 "rms_2_aform%16" (double, rms), size is 50000 dist_O2'-O4'%16 "dist_O2'-O4'%16" (double, distance), size is 50000 2pOP1%16 "2pOP1%16" (double, distance), size is 50000 z1%16 "z1%16" (double, torsion(zeta)), size is 50000 rms_2_aform%17 "rms_2_aform%17" (double, rms), size is 50000 dist_O2'-O4'%17 "dist_O2'-O4'%17" (double, distance), size is 50000 2pOP1%17 "2pOP1%17" (double, distance), size is 50000 z1%17 "z1%17" (double, torsion(zeta)), size is 50000 ---------- RUN END --------------------------------------------------- [hist z1%3,-180,180,1 2pOP1%3,0,10,0.1 free 298.41 out 2dhist_zeta-OP1.gnu] Hist: 2dhist_zeta-OP1.gnu: Set up for 2 dimensions using the following datasets: [ z1%3 2pOP1%3 ] Free energy in kcal/mol will be calculated from bin populations at 298.410000 K. ---------- RUN BEGIN ------------------------------------------------- Warning: No actions/output trajectories specified. ANALYSIS: Performing 1 analyses: 0: [hist z1%3,-180,180,1 2pOP1%3,0,10,0.1 free 298.41 out 2dhist_zeta-OP1.gnu] Dim z1%3: -180.000000->180.000000, step 1.000000, 360 bins. Dim 2pOP1%3: 0.000000->10.000000, step 0.100000, 100 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 36000 Histogram: Calculating free E at 298.410000 K. Bins max is 139 Artificial ceiling (bin pop = 0.5) is 3.337188 kcal/mol. TIME: Analyses took 0.0019 seconds. DATASETS: 74 data sets: [a-form]:1%0 "[a-form]:1" (reference), size is 1 '../../../../../A-form.pdb', refindex 0 (65 atoms) rms_2_aform%0 "rms_2_aform" (double, rms), size is 50000 dist_O2'-O4'%0 "dist_O2'-O4'" (double, distance), size is 50000 2pOP1%0 "2pOP1" (double, distance), size is 50000 z1%0 "z1" (double, torsion(zeta)), size is 50000 rms_2_aform%1 "rms_2_aform%1" (double, rms), size is 50000 dist_O2'-O4'%1 "dist_O2'-O4'%1" (double, distance), size is 50000 2pOP1%1 "2pOP1%1" (double, distance), size is 50000 z1%1 "z1%1" (double, torsion(zeta)), size is 50000 rms_2_aform%2 "rms_2_aform%2" (double, rms), size is 50000 dist_O2'-O4'%2 "dist_O2'-O4'%2" (double, distance), size is 50000 2pOP1%2 "2pOP1%2" (double, distance), size is 50000 z1%2 "z1%2" (double, torsion(zeta)), size is 50000 rms_2_aform%3 "rms_2_aform%3" (double, rms), size is 50000 dist_O2'-O4'%3 "dist_O2'-O4'%3" (double, distance), size is 50000 2pOP1%3 "2pOP1%3" (double, distance), size is 50000 z1%3 "z1%3" (double, torsion(zeta)), size is 50000 rms_2_aform%4 "rms_2_aform%4" (double, rms), size is 50000 dist_O2'-O4'%4 "dist_O2'-O4'%4" (double, distance), size is 50000 2pOP1%4 "2pOP1%4" (double, distance), size is 50000 z1%4 "z1%4" (double, torsion(zeta)), size is 50000 rms_2_aform%5 "rms_2_aform%5" (double, rms), size is 50000 dist_O2'-O4'%5 "dist_O2'-O4'%5" (double, distance), size is 50000 2pOP1%5 "2pOP1%5" (double, distance), size is 50000 z1%5 "z1%5" (double, torsion(zeta)), size is 50000 rms_2_aform%6 "rms_2_aform%6" (double, rms), size is 50000 dist_O2'-O4'%6 "dist_O2'-O4'%6" (double, distance), size is 50000 2pOP1%6 "2pOP1%6" (double, distance), size is 50000 z1%6 "z1%6" (double, torsion(zeta)), size is 50000 rms_2_aform%7 "rms_2_aform%7" (double, rms), size is 50000 dist_O2'-O4'%7 "dist_O2'-O4'%7" (double, distance), size is 50000 2pOP1%7 "2pOP1%7" (double, distance), size is 50000 z1%7 "z1%7" (double, torsion(zeta)), size is 50000 rms_2_aform%8 "rms_2_aform%8" (double, rms), size is 50000 dist_O2'-O4'%8 "dist_O2'-O4'%8" (double, distance), size is 50000 2pOP1%8 "2pOP1%8" (double, distance), size is 50000 z1%8 "z1%8" (double, torsion(zeta)), size is 50000 rms_2_aform%9 "rms_2_aform%9" (double, rms), size is 50000 dist_O2'-O4'%9 "dist_O2'-O4'%9" (double, distance), size is 50000 2pOP1%9 "2pOP1%9" (double, distance), size is 50000 z1%9 "z1%9" (double, torsion(zeta)), size is 50000 rms_2_aform%10 "rms_2_aform%10" (double, rms), size is 50000 dist_O2'-O4'%10 "dist_O2'-O4'%10" (double, distance), size is 50000 2pOP1%10 "2pOP1%10" (double, distance), size is 50000 z1%10 "z1%10" (double, torsion(zeta)), size is 50000 rms_2_aform%11 "rms_2_aform%11" (double, rms), size is 50000 dist_O2'-O4'%11 "dist_O2'-O4'%11" (double, distance), size is 50000 2pOP1%11 "2pOP1%11" (double, distance), size is 50000 z1%11 "z1%11" (double, torsion(zeta)), size is 50000 rms_2_aform%12 "rms_2_aform%12" (double, rms), size is 50000 dist_O2'-O4'%12 "dist_O2'-O4'%12" (double, distance), size is 50000 2pOP1%12 "2pOP1%12" (double, distance), size is 50000 z1%12 "z1%12" (double, torsion(zeta)), size is 50000 rms_2_aform%13 "rms_2_aform%13" (double, rms), size is 50000 dist_O2'-O4'%13 "dist_O2'-O4'%13" (double, distance), size is 50000 2pOP1%13 "2pOP1%13" (double, distance), size is 50000 z1%13 "z1%13" (double, torsion(zeta)), size is 50000 rms_2_aform%14 "rms_2_aform%14" (double, rms), size is 50000 dist_O2'-O4'%14 "dist_O2'-O4'%14" (double, distance), size is 50000 2pOP1%14 "2pOP1%14" (double, distance), size is 50000 z1%14 "z1%14" (double, torsion(zeta)), size is 50000 rms_2_aform%15 "rms_2_aform%15" (double, rms), size is 50000 dist_O2'-O4'%15 "dist_O2'-O4'%15" (double, distance), size is 50000 2pOP1%15 "2pOP1%15" (double, distance), size is 50000 z1%15 "z1%15" (double, torsion(zeta)), size is 50000 rms_2_aform%16 "rms_2_aform%16" (double, rms), size is 50000 dist_O2'-O4'%16 "dist_O2'-O4'%16" (double, distance), size is 50000 2pOP1%16 "2pOP1%16" (double, distance), size is 50000 z1%16 "z1%16" (double, torsion(zeta)), size is 50000 rms_2_aform%17 "rms_2_aform%17" (double, rms), size is 50000 dist_O2'-O4'%17 "dist_O2'-O4'%17" (double, distance), size is 50000 2pOP1%17 "2pOP1%17" (double, distance), size is 50000 z1%17 "z1%17" (double, torsion(zeta)), size is 50000 Hist_00073%17 "Hist_00073%17" (double matrix), size is 36000 DATAFILES: 2dhist_zeta-OP1.gnu (Gnuplot File): Hist_00073%17 ---------- RUN END --------------------------------------------------- TIME: Total execution time: 890.2872 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.