CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/21/16 12:29:32 | Available memory: 3.071 GB INPUT: Reading input from 'pt-analysis.bb.in' [parm ../../aa/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apa]] Reading '../../aa/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../ag/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apg]] Reading '../../ag/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../ga/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpa]] Reading '../../ga/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../gg/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpg]] Reading '../../gg/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../ac/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apc]] Reading '../../ac/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../au/tip3p/ff12sb/run1/build/noWAt.topo.hmr [apu]] Reading '../../au/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../gc/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpc]] Reading '../../gc/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../gu/tip3p/ff12sb/run1/build/noWAt.topo.hmr [gpu]] Reading '../../gu/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../ca/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpa]] Reading '../../ca/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../cg/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpg]] Reading '../../cg/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../ua/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upa]] Reading '../../ua/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../ug/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upg]] Reading '../../ug/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../cc/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpc]] Reading '../../cc/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../cu/tip3p/ff12sb/run1/build/noWAt.topo.hmr [cpu]] Reading '../../cu/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../uc/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upc]] Reading '../../uc/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [parm ../../uu/tip3p/ff12sb/run1/build/noWAt.topo.hmr [upu]] Reading '../../uu/tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [trajin ../../aa/cluster-all/km-7/ctraj.c2 parm [apa]] Reading '../../aa/cluster-all/km-7/ctraj.c2' as Amber NetCDF [trajin ../../ag/cluster-all/km-6/ctraj.c2 parm [apg]] Reading '../../ag/cluster-all/km-6/ctraj.c2' as Amber NetCDF [trajin ../../ga/cluster-1-1/km-5/ctraj.c1 parm [gpa]] Reading '../../ga/cluster-1-1/km-5/ctraj.c1' as Amber NetCDF [trajin ../../gg/cluster-all/km-6/ctraj.c0 parm [gpg]] Reading '../../gg/cluster-all/km-6/ctraj.c0' as Amber NetCDF [trajin ../../ac/cluster-all/km-7/ctraj.c0 parm [apc]] Reading '../../ac/cluster-all/km-7/ctraj.c0' as Amber NetCDF [trajin ../../au/cluster-1-1/km-5/ctraj.c0 parm [apu]] Reading '../../au/cluster-1-1/km-5/ctraj.c0' as Amber NetCDF [trajin ../../gc/cluster-1-1/km-6-bbC2/ctraj.c0 parm [gpc]] Reading '../../gc/cluster-1-1/km-6-bbC2/ctraj.c0' as Amber NetCDF [trajin ../../gu/cluster-1-1/km-6/ctraj.c0 parm [gpu]] Reading '../../gu/cluster-1-1/km-6/ctraj.c0' as Amber NetCDF [trajin ../../ca/cluster-all/km-6/ctraj.c1 parm [cpa]] Reading '../../ca/cluster-all/km-6/ctraj.c1' as Amber NetCDF [trajin ../../cg/cluster-1-1/km-6-bbC2/ctraj.c0 parm [cpg]] Reading '../../cg/cluster-1-1/km-6-bbC2/ctraj.c0' as Amber NetCDF [trajin ../../ua/cluster-1-1/km-7/ctraj.c0 parm [upa]] Reading '../../ua/cluster-1-1/km-7/ctraj.c0' as Amber NetCDF [trajin ../../ug/cluster-1-1/km-6/ctraj.c0 parm [upg]] Reading '../../ug/cluster-1-1/km-6/ctraj.c0' as Amber NetCDF [trajin ../../cc/cluster-all/km-5/ctraj.c0 parm [cpc]] Reading '../../cc/cluster-all/km-5/ctraj.c0' as Amber NetCDF [trajin ../../cu/cluster-1-1/km-5-bbC2/ctraj.c0 parm [cpu]] Reading '../../cu/cluster-1-1/km-5-bbC2/ctraj.c0' as Amber NetCDF [trajin ../../uc/cluster-1-1/km-5/ctraj.c1 parm [upc]] Reading '../../uc/cluster-1-1/km-5/ctraj.c1' as Amber NetCDF [trajin ../../uu/cluster-all/km-5/ctraj.c1 parm [upu]] Reading '../../uu/cluster-all/km-5/ctraj.c1' as Amber NetCDF [distance dist1 :1@HO2' :2@O5'] DISTANCE: :1@HO2' to :2@O5', center of mass. [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] DIHEDRAL: [:1@C5']-[:1@C4']-[:1@C3']-[:1@O3'] Output range is -180 to 180 degrees. [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] DIHEDRAL: [:2@C5']-[:2@C4']-[:2@C3']-[:2@O3'] Output range is -180 to 180 degrees. [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] DIHEDRAL: [:1@C4']-[:1@C3']-[:1@O3']-[:2@P] Output range is -180 to 180 degrees. [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. [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] DIHEDRAL: [:1@O3']-[:2@P]-[:2@O5']-[:2@C5'] Output range is -180 to 180 degrees. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (16 total): 0: [apa] noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol 1: [apg] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol 2: [gpa] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol 3: [gpg] noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol 4: [apc] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol 5: [apu] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol 6: [gpc] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol 7: [gpu] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol 8: [cpa] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol 9: [cpg] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol 10: [upa] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol 11: [upg] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol 12: [cpc] noWAt.topo.hmr, 61 atoms, 2 res, box: Orthogonal, 1 mol 13: [cpu] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol 14: [upc] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol 15: [upu] noWAt.topo.hmr, 59 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (16 total): 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 111938 of 111938) 1: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 99258 of 99258) 2: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 31448 of 31448) 3: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 203546 of 203546) 4: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 230147 of 230147) 5: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 41061 of 41061) 6: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 47347 of 47347) 7: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 56497 of 56497) 8: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 145142 of 145142) 9: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 40201 of 40201) 10: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 50866 of 50866) 11: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 49458 of 49458) 12: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 273041 of 273041) 13: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 55868 of 55868) 14: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 27062 of 27062) 15: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 126351 of 126351) Coordinate processing will occur on 1589231 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist1 :1@HO2' :2@O5'] :1@HO2' (1 atoms) to :2@O5' (1 atoms), imaged. 1: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 2: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c2 (1-111938, 1) ----- 0% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist1 :1@HO2' :2@O5'] :1@HO2' (1 atoms) to :2@O5' (1 atoms), imaged. 1: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 2: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c2 (1-99258, 1) ----- 10% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist1 :1@HO2' :2@O5'] :1@HO2' (1 atoms) to :2@O5' (1 atoms), imaged. 1: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 2: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c1 (1-31448, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist1 :1@HO2' :2@O5'] :1@HO2' (1 atoms) to :2@O5' (1 atoms), imaged. 1: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 2: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c0 (1-203546, 1) ----- 20% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist1 :1@HO2' :2@O5'] :1@HO2' (1 atoms) to :2@O5' (1 atoms), imaged. 1: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 2: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c0 (1-230147, 1) ----- 30% 40% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist1 :1@HO2' :2@O5'] :1@HO2' (1 atoms) to :2@O5' (1 atoms), imaged. 1: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 2: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c0 (1-41061, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist1 :1@HO2' :2@O5'] :1@HO2' (1 atoms) to :2@O5' (1 atoms), imaged. 1: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 2: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c0 (1-47347, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist1 :1@HO2' :2@O5'] :1@HO2' (1 atoms) to :2@O5' (1 atoms), imaged. 1: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 2: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c0 (1-56497, 1) ----- 50% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist1 :1@HO2' :2@O5'] :1@HO2' (1 atoms) to :2@O5' (1 atoms), imaged. 1: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 2: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c1 (1-145142, 1) ----- 60% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist1 :1@HO2' :2@O5'] :1@HO2' (1 atoms) to :2@O5' (1 atoms), imaged. 1: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 2: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c0 (1-40201, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist1 :1@HO2' :2@O5'] :1@HO2' (1 atoms) to :2@O5' (1 atoms), imaged. 1: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 2: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c0 (1-50866, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist1 :1@HO2' :2@O5'] :1@HO2' (1 atoms) to :2@O5' (1 atoms), imaged. 1: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 2: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c0 (1-49458, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist1 :1@HO2' :2@O5'] :1@HO2' (1 atoms) to :2@O5' (1 atoms), imaged. 1: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 2: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c0 (1-273041, 1) ----- 70% 80% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist1 :1@HO2' :2@O5'] :1@HO2' (1 atoms) to :2@O5' (1 atoms), imaged. 1: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 2: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c0 (1-55868, 1) ----- 90% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist1 :1@HO2' :2@O5'] :1@HO2' (1 atoms) to :2@O5' (1 atoms), imaged. 1: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 2: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c1 (1-27062, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist1 :1@HO2' :2@O5'] :1@HO2' (1 atoms) to :2@O5' (1 atoms), imaged. 1: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 2: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 3: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 4: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) ----- ctraj.c1 (1-126351, 1) ----- 100% Complete. Read 1589231 frames and processed 1589231 frames. TIME: Avg. throughput= 534838.1786 frames / second. ACTION OUTPUT: DATASETS (6 total): dist1 "dist1" (double, distance), size is 1589231 d1 "d1" (double, torsion(delta)), size is 1589231 d2 "d2" (double, torsion(delta)), size is 1589231 e1 "e1" (double, torsion(epsilon)), size is 1589231 z1 "z1" (double, torsion(zeta)), size is 1589231 a2 "a2" (double, torsion(alpha)), size is 1589231 RUN TIMING: TIME: Init : 0.0019 s ( 0.06%) TIME: Trajectory Process : 2.9714 s ( 99.93%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 2.9734 s ---------- RUN END --------------------------------------------------- [hist e1,-180,180,0.5 dist1,0,6,0.01 out 2dhist_e1_dist1.gnu norm] Hist: 2dhist_e1_dist1.gnu: Set up for 2 dimensions using the following datasets: [ e1 dist1 ] norm: Sum over bins will be normalized to 1.0. [hist z1,-180,180,0.5 a2,-180,180,0.5 out 2dhist_z1_a2.gnu norm] Hist: 2dhist_z1_a2.gnu: Set up for 2 dimensions using the following datasets: [ z1 a2 ] norm: Sum over bins will be normalized to 1.0. [hist e1,-180,180,0.5 d1,-180,180,0.5 out 2dhist_e1_d1.gnu norm] Hist: 2dhist_e1_d1.gnu: Set up for 2 dimensions using the following datasets: [ e1 d1 ] norm: Sum over bins will be normalized to 1.0. [hist e1,-180,180,0.5 z1,-180,180,0.5 out 2dhist_e1_z1.gnu norm] Hist: 2dhist_e1_z1.gnu: Set up for 2 dimensions using the following datasets: [ e1 z1 ] norm: Sum over bins will be normalized to 1.0. ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (16 total): 0: [apa] noWAt.topo.hmr, 65 atoms, 2 res, box: Orthogonal, 1 mol 1: [apg] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol 2: [gpa] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol 3: [gpg] noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol 4: [apc] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol 5: [apu] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol 6: [gpc] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol 7: [gpu] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol 8: [cpa] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol 9: [cpg] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol 10: [upa] noWAt.topo.hmr, 62 atoms, 2 res, box: Orthogonal, 1 mol 11: [upg] noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol 12: [cpc] noWAt.topo.hmr, 61 atoms, 2 res, box: Orthogonal, 1 mol 13: [cpu] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol 14: [upc] noWAt.topo.hmr, 60 atoms, 2 res, box: Orthogonal, 1 mol 15: [upu] noWAt.topo.hmr, 59 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (16 total): 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 111938 of 111938) 1: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 99258 of 99258) 2: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 31448 of 31448) 3: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 203546 of 203546) 4: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 230147 of 230147) 5: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 41061 of 41061) 6: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 47347 of 47347) 7: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 56497 of 56497) 8: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 145142 of 145142) 9: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 40201 of 40201) 10: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 50866 of 50866) 11: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 49458 of 49458) 12: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 273041 of 273041) 13: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 55868 of 55868) 14: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 27062 of 27062) 15: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 126351 of 126351) Coordinate processing will occur on 1589231 frames. BEGIN TRAJECTORY PROCESSING: ----- ctraj.c2 (1-111938, 1) ----- 0% ----- ctraj.c2 (1-99258, 1) ----- 10% ----- ctraj.c1 (1-31448, 1) ----- ----- ctraj.c0 (1-203546, 1) ----- 20% ----- ctraj.c0 (1-230147, 1) ----- 30% 40% ----- ctraj.c0 (1-41061, 1) ----- ----- ctraj.c0 (1-47347, 1) ----- ----- ctraj.c0 (1-56497, 1) ----- 50% ----- ctraj.c1 (1-145142, 1) ----- 60% ----- ctraj.c0 (1-40201, 1) ----- ----- ctraj.c0 (1-50866, 1) ----- ----- ctraj.c0 (1-49458, 1) ----- ----- ctraj.c0 (1-273041, 1) ----- 70% 80% ----- ctraj.c0 (1-55868, 1) ----- 90% ----- ctraj.c1 (1-27062, 1) ----- ----- ctraj.c1 (1-126351, 1) ----- 100% Complete. Read 1589231 frames and processed 1589231 frames. TIME: Avg. throughput= 994713.5748 frames / second. ACTION OUTPUT: ANALYSIS: Performing 4 analyses: 0: [hist e1,-180,180,0.5 dist1,0,6,0.01 out 2dhist_e1_dist1.gnu norm] Calculating bins from min=-180 max=180 step=0.5. Dim e1: -180.000000->180.000000, step 0.500000, 720 bins. Calculating bins from min=0 max=6 step=0.01. Dim dist1: 0.000000->6.000000, step 0.010000, 600 bins. Hist: 1589231 data points in each dimension. Hist: Allocating histogram, total bins = 432000 Warning: Frame 3095 Coordinates out of bounds (-1) Warning: Frame 16813 Coordinates out of bounds (-1) Warning: Frame 56481 Coordinates out of bounds (-1) Warning: Frame 56543 Coordinates out of bounds (-1) Warning: Frame 60514 Coordinates out of bounds (-1) Warning: Frame 65493 Coordinates out of bounds (-1) Warning: Frame 67108 Coordinates out of bounds (-1) Warning: Frame 68603 Coordinates out of bounds (-1) Warning: Frame 69205 Coordinates out of bounds (-1) Warning: Frame 70371 Coordinates out of bounds (-1) Warning: Frame 71028 Coordinates out of bounds (-1) Warning: Frame 72914 Coordinates out of bounds (-1) Warning: Frame 72916 Coordinates out of bounds (-1) Warning: Frame 72955 Coordinates out of bounds (-1) Warning: Frame 73842 Coordinates out of bounds (-1) Warning: Frame 74329 Coordinates out of bounds (-1) Warning: Frame 79305 Coordinates out of bounds (-1) Warning: Frame 80844 Coordinates out of bounds (-1) Warning: Frame 82543 Coordinates out of bounds (-1) Warning: Frame 91399 Coordinates out of bounds (-1) Warning: Frame 101278 Coordinates out of bounds (-1) Warning: Frame 167597 Coordinates out of bounds (-1) Warning: Frame 170392 Coordinates out of bounds (-1) Warning: Frame 171496 Coordinates out of bounds (-1) Warning: Frame 171505 Coordinates out of bounds (-1) Warning: Frame 171512 Coordinates out of bounds (-1) Warning: Frame 172140 Coordinates out of bounds (-1) Warning: Frame 174220 Coordinates out of bounds (-1) Warning: Frame 192522 Coordinates out of bounds (-1) Warning: Frame 200312 Coordinates out of bounds (-1) Warning: Frame 219594 Coordinates out of bounds (-1) Warning: Frame 285364 Coordinates out of bounds (-1) Warning: Frame 294448 Coordinates out of bounds (-1) Warning: Frame 309514 Coordinates out of bounds (-1) Warning: Frame 338647 Coordinates out of bounds (-1) Warning: Frame 359377 Coordinates out of bounds (-1) Warning: Frame 363473 Coordinates out of bounds (-1) Warning: Frame 366079 Coordinates out of bounds (-1) Warning: Frame 397828 Coordinates out of bounds (-1) Warning: Frame 450545 Coordinates out of bounds (-1) Warning: Frame 457935 Coordinates out of bounds (-1) Warning: Frame 473103 Coordinates out of bounds (-1) Warning: Frame 473487 Coordinates out of bounds (-1) Warning: Frame 483213 Coordinates out of bounds (-1) Warning: Frame 495717 Coordinates out of bounds (-1) Warning: Frame 514266 Coordinates out of bounds (-1) Warning: Frame 550740 Coordinates out of bounds (-1) Warning: Frame 590336 Coordinates out of bounds (-1) Warning: Frame 593911 Coordinates out of bounds (-1) Warning: Frame 593912 Coordinates out of bounds (-1) Warning: Frame 611516 Coordinates out of bounds (-1) Warning: Frame 612296 Coordinates out of bounds (-1) Warning: Frame 620697 Coordinates out of bounds (-1) Warning: Frame 623576 Coordinates out of bounds (-1) Warning: Frame 644074 Coordinates out of bounds (-1) Warning: Frame 675344 Coordinates out of bounds (-1) Warning: Frame 677130 Coordinates out of bounds (-1) Warning: Frame 689414 Coordinates out of bounds (-1) Warning: Frame 695360 Coordinates out of bounds (-1) Warning: Frame 713568 Coordinates out of bounds (-1) Warning: Frame 740377 Coordinates out of bounds (-1) Warning: Frame 749297 Coordinates out of bounds (-1) Warning: Frame 751912 Coordinates out of bounds (-1) Warning: Frame 761724 Coordinates out of bounds (-1) Warning: Frame 766072 Coordinates out of bounds (-1) Warning: Frame 792516 Coordinates out of bounds (-1) Warning: Frame 794061 Coordinates out of bounds (-1) Warning: Frame 800637 Coordinates out of bounds (-1) Warning: Frame 836643 Coordinates out of bounds (-1) Warning: Frame 836644 Coordinates out of bounds (-1) Warning: Frame 897319 Coordinates out of bounds (-1) Warning: Frame 900525 Coordinates out of bounds (-1) Warning: Frame 904555 Coordinates out of bounds (-1) Warning: Frame 907420 Coordinates out of bounds (-1) Warning: Frame 907609 Coordinates out of bounds (-1) Warning: Frame 911226 Coordinates out of bounds (-1) Warning: Frame 983463 Coordinates out of bounds (-1) Warning: Frame 987309 Coordinates out of bounds (-1) Warning: Frame 1076907 Coordinates out of bounds (-1) Warning: Frame 1085967 Coordinates out of bounds (-1) Warning: Frame 1178415 Coordinates out of bounds (-1) Warning: Frame 1181879 Coordinates out of bounds (-1) Warning: Frame 1189090 Coordinates out of bounds (-1) Warning: Frame 1255691 Coordinates out of bounds (-1) Warning: Frame 1283502 Coordinates out of bounds (-1) Warning: Frame 1463942 Coordinates out of bounds (-1) Warning: Frame 1528302 Coordinates out of bounds (-1) Warning: Frame 1536244 Coordinates out of bounds (-1) Warning: Frame 1537238 Coordinates out of bounds (-1) Warning: Frame 1537466 Coordinates out of bounds (-1) Warning: Frame 1540045 Coordinates out of bounds (-1) Warning: Frame 1540225 Coordinates out of bounds (-1) Warning: Frame 1540739 Coordinates out of bounds (-1) Warning: Frame 1549689 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 1.58914e+06 1: [hist z1,-180,180,0.5 a2,-180,180,0.5 out 2dhist_z1_a2.gnu norm] Calculating bins from min=-180 max=180 step=0.5. Dim z1: -180.000000->180.000000, step 0.500000, 720 bins. Calculating bins from min=-180 max=180 step=0.5. Dim a2: -180.000000->180.000000, step 0.500000, 720 bins. Hist: 1589231 data points in each dimension. Hist: Allocating histogram, total bins = 518400 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 1.58923e+06 2: [hist e1,-180,180,0.5 d1,-180,180,0.5 out 2dhist_e1_d1.gnu norm] Calculating bins from min=-180 max=180 step=0.5. Dim e1: -180.000000->180.000000, step 0.500000, 720 bins. Calculating bins from min=-180 max=180 step=0.5. Dim d1: -180.000000->180.000000, step 0.500000, 720 bins. Hist: 1589231 data points in each dimension. Hist: Allocating histogram, total bins = 518400 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 1.58923e+06 3: [hist e1,-180,180,0.5 z1,-180,180,0.5 out 2dhist_e1_z1.gnu norm] Calculating bins from min=-180 max=180 step=0.5. Dim e1: -180.000000->180.000000, step 0.500000, 720 bins. Calculating bins from min=-180 max=180 step=0.5. Dim z1: -180.000000->180.000000, step 0.500000, 720 bins. Hist: 1589231 data points in each dimension. Hist: Allocating histogram, total bins = 518400 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 1.58923e+06 TIME: Analyses took 0.1338 seconds. DATASETS (10 total): dist1 "dist1" (double, distance), size is 1589231 d1 "d1" (double, torsion(delta)), size is 1589231 d2 "d2" (double, torsion(delta)), size is 1589231 e1 "e1" (double, torsion(epsilon)), size is 1589231 z1 "z1" (double, torsion(zeta)), size is 1589231 a2 "a2" (double, torsion(alpha)), size is 1589231 Hist_00022 "Hist_00022" (double matrix), size is 432000 Hist_00023 "Hist_00023" (double matrix), size is 518400 Hist_00024 "Hist_00024" (double matrix), size is 518400 Hist_00025 "Hist_00025" (double matrix), size is 518400 DATAFILES (4 total): 2dhist_e1_dist1.gnu (Gnuplot File): Hist_00022 2dhist_z1_a2.gnu (Gnuplot File): Hist_00023 2dhist_e1_d1.gnu (Gnuplot File): Hist_00024 2dhist_e1_z1.gnu (Gnuplot File): Hist_00025 RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 1.5977 s ( 30.06%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.1338 s ( 2.52%) TIME: Data File Write : 3.5826 s ( 67.41%) TIME: Other : 0.0006 s ( 0.00%) TIME: Run Total 5.3148 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 8.3979 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.