CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/28/17 16:29:11 | Available memory: 119189 MB INPUT: Reading Input from STDIN [parm /scratch/foxt/AMD/aMD_SEFTIG/vac.seftig_solv.top] Reading '/scratch/foxt/AMD/aMD_SEFTIG/vac.seftig_solv.top' as Amber Topology [trajin /scratch/foxt/AMD/aMD_SEFTIG/vac.amd.traj.nc 1 1 ] Reading '/scratch/foxt/AMD/aMD_SEFTIG/vac.amd.traj.nc' as Amber NetCDF [readdata 01_dihe-traj.dat10 name BB] Reading '01_dihe-traj.dat10' as Standard Data File with name 'BB' DataFile 01_dihe-traj.dat10 has 13 columns, 11 lines. DataFile contains labels: 1: Frame 2: Phi_1 3: Psi_1 4: Ome_1 5: Phi_2 6: Psi_2 7: Ome_2 8: Phi_3 9: Psi_3 10: Ome_3 11: Phi_4 12: Psi_4 13: Ome_4 Index column is 1 [dataset BB[*] mode torsion ] DataSet mode = torsion 'Phi_1' 'Psi_1' 'Ome_1' 'Phi_2' 'Psi_2' 'Ome_2' 'Phi_3' 'Psi_3' 'Ome_3' 'Phi_4' 'Psi_4' 'Ome_4' [matrix dihcovar dihedrals BB[*] out 02_covar-dihedrals.dat name DIH] MATRIX: Calculating dihedral covariance matrix, output is by atom. 12 data sets. Printing to file 02_covar-dihedrals.dat Matrix data set is 'DIH' Start: 1 Stop: Final frame [list ] ACTIONS: 0: [matrix dihcovar dihedrals BB[*] out 02_covar-dihedrals.dat name DIH] INPUT TRAJECTORIES: 0: 'vac.amd.traj.nc' is a NetCDF AMBER trajectory, Parm vac.seftig_solv.top (Trunc. Oct. box) (reading 1 of 50000) Coordinate processing will occur on 1 frames. PARAMETER FILES: 0: 'vac.seftig_solv.top', 42 atoms, 4 res, box: Trunc. Oct., 1 mol, 1 frames DATAFILES: 02_covar-dihedrals.dat (Standard Data File): DIH DATASETS: 13 data sets: BB:2 "Phi_1" (double, torsion), size is 10 BB:3 "Psi_1" (double, torsion), size is 10 BB:4 "Ome_1" (double, torsion), size is 10 BB:5 "Phi_2" (double, torsion), size is 10 BB:6 "Psi_2" (double, torsion), size is 10 BB:7 "Ome_2" (double, torsion), size is 10 BB:8 "Phi_3" (double, torsion), size is 10 BB:9 "Psi_3" (double, torsion), size is 10 BB:10 "Ome_3" (double, torsion), size is 10 BB:11 "Phi_4" (double, torsion), size is 10 BB:12 "Psi_4" (double, torsion), size is 10 BB:13 "Ome_4" (double, torsion), size is 10 DIH "DIH" (double matrix, matrix(dihedral covariance)), size is 0 [diagmatrix DIH vecs 10 out 02_evecs_dihedrals.dat name DIHMODES] Changed DataFile '02_evecs_dihedrals.dat' type to Evecs file for set DIHMODES DIAGMATRIX: Diagonalizing matrix DIH and writing modes to 02_evecs_dihedrals.dat Calculating 10 eigenvectors Storing modes with name: DIHMODES [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: 'vac.seftig_solv.top', 42 atoms, 4 res, box: Trunc. Oct., 1 mol, 1 frames INPUT TRAJECTORIES: 0: 'vac.amd.traj.nc' is a NetCDF AMBER trajectory, Parm vac.seftig_solv.top (Trunc. Oct. box) (reading 1 of 50000) Coordinate processing will occur on 1 frames. TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'vac.seftig_solv.top' (1 actions): 0: [matrix dihcovar dihedrals BB[*] out 02_covar-dihedrals.dat name DIH] ----- vac.amd.traj.nc (1-1, 1) ----- 100% Complete. Read 1 frames and processed 1 frames. TIME: Trajectory processing: 0.0013 s TIME: Avg. throughput= 779.4232 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [diagmatrix DIH vecs 10 out 02_evecs_dihedrals.dat name DIHMODES] Warning: In matrix 'DIH', # of frames 1 is less than # of columns 24. Warning: The max # of non-zero eigenvalues will be 1 TIME: Analyses took 0.0005 seconds. DATASETS: 14 data sets: BB:2 "Phi_1" (double, torsion), size is 10 BB:3 "Psi_1" (double, torsion), size is 10 BB:4 "Ome_1" (double, torsion), size is 10 BB:5 "Phi_2" (double, torsion), size is 10 BB:6 "Psi_2" (double, torsion), size is 10 BB:7 "Ome_2" (double, torsion), size is 10 BB:8 "Phi_3" (double, torsion), size is 10 BB:9 "Psi_3" (double, torsion), size is 10 BB:10 "Ome_3" (double, torsion), size is 10 BB:11 "Phi_4" (double, torsion), size is 10 BB:12 "Psi_4" (double, torsion), size is 10 BB:13 "Ome_4" (double, torsion), size is 10 DIH "DIH" (double matrix, matrix(dihedral covariance)), size is 300 DIHMODES "DIHMODES" (eigenmodes(dihedral covariance)), size is 10 DATAFILES: 02_covar-dihedrals.dat (Standard Data File): DIH 02_evecs_dihedrals.dat (Evecs file): DIHMODES ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.0204 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.