CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/21/16 15:48:17 | Available memory: 2.496 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.c1 parm [apa]] Reading '../../aa/cluster-all/km-7/ctraj.c1' as Amber NetCDF [trajin ../../ag/cluster-all/km-6/ctraj.c0 parm [apg]] Reading '../../ag/cluster-all/km-6/ctraj.c0' as Amber NetCDF [trajin ../../ga/cluster-1-1/km-5/ctraj.c0 parm [gpa]] Reading '../../ga/cluster-1-1/km-5/ctraj.c0' as Amber NetCDF [trajin ../../gg/cluster-all/km-6/ctraj.c1 parm [gpg]] Reading '../../gg/cluster-all/km-6/ctraj.c1' as Amber NetCDF [trajin ../../ac/cluster-all/km-7/ctraj.c1 parm [apc]] Reading '../../ac/cluster-all/km-7/ctraj.c1' as Amber NetCDF [trajin ../../au/cluster-1-1/km-5/ctraj.c1 parm [apu]] Reading '../../au/cluster-1-1/km-5/ctraj.c1' as Amber NetCDF [trajin ../../gc/cluster-1-1/km-6-bbC2/ctraj.c1 parm [gpc]] Reading '../../gc/cluster-1-1/km-6-bbC2/ctraj.c1' as Amber NetCDF [trajin ../../gu/cluster-1-1/km-6/ctraj.c2 parm [gpu]] Reading '../../gu/cluster-1-1/km-6/ctraj.c2' as Amber NetCDF [trajin ../../ca/cluster-all/km-6/ctraj.c3 parm [cpa]] Reading '../../ca/cluster-all/km-6/ctraj.c3' as Amber NetCDF [trajin ../../cg/cluster-1-1/km-6-bbC2/ctraj.c3 parm [cpg]] Reading '../../cg/cluster-1-1/km-6-bbC2/ctraj.c3' as Amber NetCDF [trajin ../../ua/cluster-1-1/km-7/ctraj.c3 parm [upa]] Reading '../../ua/cluster-1-1/km-7/ctraj.c3' as Amber NetCDF [trajin ../../ug/cluster-1-1/km-6/ctraj.c3 parm [upg]] Reading '../../ug/cluster-1-1/km-6/ctraj.c3' as Amber NetCDF [trajin ../../cc/cluster-all/km-5/ctraj.c3 parm [cpc]] Reading '../../cc/cluster-all/km-5/ctraj.c3' as Amber NetCDF [trajin ../../cu/cluster-1-1/km-5-bbC2/ctraj.c4 parm [cpu]] Reading '../../cu/cluster-1-1/km-5-bbC2/ctraj.c4' as Amber NetCDF [trajin ../../uc/cluster-1-1/km-5/ctraj.c3 parm [upc]] Reading '../../uc/cluster-1-1/km-5/ctraj.c3' as Amber NetCDF [trajin ../../uu/cluster-all/km-5/ctraj.c2 parm [upu]] Reading '../../uu/cluster-all/km-5/ctraj.c2' as Amber NetCDF [distance dist2 :1@HO2' :2@OP1] DISTANCE: :1@HO2' to :2@OP1, 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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 164404 of 164404) 1: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 228792 of 228792) 2: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 34167 of 34167) 3: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 189697 of 189697) 4: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 109439 of 109439) 5: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 19943 of 19943) 6: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 24389 of 24389) 7: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 12720 of 12720) 8: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 77630 of 77630) 9: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 12023 of 12023) 10: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 6487 of 6487) 11: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 5656 of 5656) 12: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 67544 of 67544) 13: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7482 of 7482) 14: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 11047 of 11047) 15: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 90296 of 90296) Coordinate processing will occur on 1061716 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist2 :1@HO2' :2@OP1] :1@HO2' (1 atoms) to :2@OP1 (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 (1-164404, 1) ----- 0% 10% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist2 :1@HO2' :2@OP1] :1@HO2' (1 atoms) to :2@OP1 (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 (1-228792, 1) ----- 20% 30% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist2 :1@HO2' :2@OP1] :1@HO2' (1 atoms) to :2@OP1 (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 (1-34167, 1) ----- 40% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist2 :1@HO2' :2@OP1] :1@HO2' (1 atoms) to :2@OP1 (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 (1-189697, 1) ----- 50% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist2 :1@HO2' :2@OP1] :1@HO2' (1 atoms) to :2@OP1 (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 (1-109439, 1) ----- 60% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist2 :1@HO2' :2@OP1] :1@HO2' (1 atoms) to :2@OP1 (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 (1-19943, 1) ----- 70% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist2 :1@HO2' :2@OP1] :1@HO2' (1 atoms) to :2@OP1 (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 (1-24389, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist2 :1@HO2' :2@OP1] :1@HO2' (1 atoms) to :2@OP1 (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 (1-12720, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist2 :1@HO2' :2@OP1] :1@HO2' (1 atoms) to :2@OP1 (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.c3 (1-77630, 1) ----- 80% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist2 :1@HO2' :2@OP1] :1@HO2' (1 atoms) to :2@OP1 (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.c3 (1-12023, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist2 :1@HO2' :2@OP1] :1@HO2' (1 atoms) to :2@OP1 (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.c3 (1-6487, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist2 :1@HO2' :2@OP1] :1@HO2' (1 atoms) to :2@OP1 (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.c3 (1-5656, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist2 :1@HO2' :2@OP1] :1@HO2' (1 atoms) to :2@OP1 (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.c3 (1-67544, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist2 :1@HO2' :2@OP1] :1@HO2' (1 atoms) to :2@OP1 (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.c4 (1-7482, 1) ----- 90% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist2 :1@HO2' :2@OP1] :1@HO2' (1 atoms) to :2@OP1 (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.c3 (1-11047, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (6 actions): 0: [distance dist2 :1@HO2' :2@OP1] :1@HO2' (1 atoms) to :2@OP1 (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 (1-90296, 1) ----- 100% Complete. Read 1061716 frames and processed 1061716 frames. TIME: Avg. throughput= 486187.5721 frames / second. ACTION OUTPUT: DATASETS (6 total): dist2 "dist2" (double, distance), size is 1061716 d1 "d1" (double, torsion(delta)), size is 1061716 d2 "d2" (double, torsion(delta)), size is 1061716 e1 "e1" (double, torsion(epsilon)), size is 1061716 z1 "z1" (double, torsion(zeta)), size is 1061716 a2 "a2" (double, torsion(alpha)), size is 1061716 RUN TIMING: TIME: Init : 0.0019 s ( 0.09%) TIME: Trajectory Process : 2.1838 s ( 99.91%) 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 2.1857 s ---------- RUN END --------------------------------------------------- [hist e1,-180,180,0.5 dist2,0,6,0.01 out 2dhist_e1_dist2.gnu norm] Hist: 2dhist_e1_dist2.gnu: Set up for 2 dimensions using the following datasets: [ e1 dist2 ] norm: Sum over bins will be normalized to 1.0. [hist z1,-180,180,0.5 dist2,0,6,0.01 out 2dhist_z1_dist2.gnu norm] Hist: 2dhist_z1_dist2.gnu: Set up for 2 dimensions using the following datasets: [ z1 dist2 ] 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 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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 164404 of 164404) 1: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 228792 of 228792) 2: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 34167 of 34167) 3: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 189697 of 189697) 4: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 109439 of 109439) 5: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 19943 of 19943) 6: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 24389 of 24389) 7: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 12720 of 12720) 8: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 77630 of 77630) 9: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 12023 of 12023) 10: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 6487 of 6487) 11: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 5656 of 5656) 12: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 67544 of 67544) 13: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7482 of 7482) 14: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 11047 of 11047) 15: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 90296 of 90296) Coordinate processing will occur on 1061716 frames. BEGIN TRAJECTORY PROCESSING: ----- ctraj.c1 (1-164404, 1) ----- 0% 10% ----- ctraj.c0 (1-228792, 1) ----- 20% 30% ----- ctraj.c0 (1-34167, 1) ----- 40% ----- ctraj.c1 (1-189697, 1) ----- 50% ----- ctraj.c1 (1-109439, 1) ----- 60% ----- ctraj.c1 (1-19943, 1) ----- 70% ----- ctraj.c1 (1-24389, 1) ----- ----- ctraj.c2 (1-12720, 1) ----- ----- ctraj.c3 (1-77630, 1) ----- 80% ----- ctraj.c3 (1-12023, 1) ----- ----- ctraj.c3 (1-6487, 1) ----- ----- ctraj.c3 (1-5656, 1) ----- ----- ctraj.c3 (1-67544, 1) ----- ----- ctraj.c4 (1-7482, 1) ----- 90% ----- ctraj.c3 (1-11047, 1) ----- ----- ctraj.c2 (1-90296, 1) ----- 100% Complete. Read 1061716 frames and processed 1061716 frames. TIME: Avg. throughput= 987333.2732 frames / second. ACTION OUTPUT: ANALYSIS: Performing 4 analyses: 0: [hist e1,-180,180,0.5 dist2,0,6,0.01 out 2dhist_e1_dist2.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 dist2: 0.000000->6.000000, step 0.010000, 600 bins. Hist: 1061716 data points in each dimension. Hist: Allocating histogram, total bins = 432000 Warning: Frame 1897 Coordinates out of bounds (-1) Warning: Frame 3467 Coordinates out of bounds (-1) Warning: Frame 10771 Coordinates out of bounds (-1) Warning: Frame 15297 Coordinates out of bounds (-1) Warning: Frame 16379 Coordinates out of bounds (-1) Warning: Frame 16381 Coordinates out of bounds (-1) Warning: Frame 22615 Coordinates out of bounds (-1) Warning: Frame 23242 Coordinates out of bounds (-1) Warning: Frame 31554 Coordinates out of bounds (-1) Warning: Frame 42997 Coordinates out of bounds (-1) Warning: Frame 51649 Coordinates out of bounds (-1) Warning: Frame 64963 Coordinates out of bounds (-1) Warning: Frame 67427 Coordinates out of bounds (-1) Warning: Frame 70891 Coordinates out of bounds (-1) Warning: Frame 71669 Coordinates out of bounds (-1) Warning: Frame 74573 Coordinates out of bounds (-1) Warning: Frame 76300 Coordinates out of bounds (-1) Warning: Frame 78502 Coordinates out of bounds (-1) Warning: Frame 80210 Coordinates out of bounds (-1) Warning: Frame 85246 Coordinates out of bounds (-1) Warning: Frame 86185 Coordinates out of bounds (-1) Warning: Frame 89273 Coordinates out of bounds (-1) Warning: Frame 91427 Coordinates out of bounds (-1) Warning: Frame 91591 Coordinates out of bounds (-1) Warning: Frame 91896 Coordinates out of bounds (-1) Warning: Frame 92058 Coordinates out of bounds (-1) Warning: Frame 92443 Coordinates out of bounds (-1) Warning: Frame 92751 Coordinates out of bounds (-1) Warning: Frame 93529 Coordinates out of bounds (-1) Warning: Frame 93738 Coordinates out of bounds (-1) Warning: Frame 95009 Coordinates out of bounds (-1) Warning: Frame 95085 Coordinates out of bounds (-1) Warning: Frame 95164 Coordinates out of bounds (-1) Warning: Frame 95510 Coordinates out of bounds (-1) Warning: Frame 95597 Coordinates out of bounds (-1) Warning: Frame 96266 Coordinates out of bounds (-1) Warning: Frame 97899 Coordinates out of bounds (-1) Warning: Frame 98303 Coordinates out of bounds (-1) Warning: Frame 98310 Coordinates out of bounds (-1) Warning: Frame 98367 Coordinates out of bounds (-1) Warning: Frame 98591 Coordinates out of bounds (-1) Warning: Frame 98900 Coordinates out of bounds (-1) Warning: Frame 99458 Coordinates out of bounds (-1) Warning: Frame 99652 Coordinates out of bounds (-1) Warning: Frame 99821 Coordinates out of bounds (-1) Warning: Frame 102834 Coordinates out of bounds (-1) Warning: Frame 103238 Coordinates out of bounds (-1) Warning: Frame 103434 Coordinates out of bounds (-1) Warning: Frame 103631 Coordinates out of bounds (-1) Warning: Frame 103793 Coordinates out of bounds (-1) Warning: Frame 103989 Coordinates out of bounds (-1) Warning: Frame 104729 Coordinates out of bounds (-1) Warning: Frame 105121 Coordinates out of bounds (-1) Warning: Frame 106185 Coordinates out of bounds (-1) Warning: Frame 106712 Coordinates out of bounds (-1) Warning: Frame 107973 Coordinates out of bounds (-1) Warning: Frame 108372 Coordinates out of bounds (-1) Warning: Frame 108446 Coordinates out of bounds (-1) Warning: Frame 108712 Coordinates out of bounds (-1) Warning: Frame 108713 Coordinates out of bounds (-1) Warning: Frame 109378 Coordinates out of bounds (-1) Warning: Frame 129299 Coordinates out of bounds (-1) Warning: Frame 142413 Coordinates out of bounds (-1) Warning: Frame 152586 Coordinates out of bounds (-1) Warning: Frame 154059 Coordinates out of bounds (-1) Warning: Frame 163537 Coordinates out of bounds (-1) Warning: Frame 163775 Coordinates out of bounds (-1) Warning: Frame 178687 Coordinates out of bounds (-1) Warning: Frame 180941 Coordinates out of bounds (-1) Warning: Frame 183160 Coordinates out of bounds (-1) Warning: Frame 207032 Coordinates out of bounds (-1) Warning: Frame 214800 Coordinates out of bounds (-1) Warning: Frame 224899 Coordinates out of bounds (-1) Warning: Frame 228979 Coordinates out of bounds (-1) Warning: Frame 240259 Coordinates out of bounds (-1) Warning: Frame 242752 Coordinates out of bounds (-1) Warning: Frame 243287 Coordinates out of bounds (-1) Warning: Frame 245974 Coordinates out of bounds (-1) Warning: Frame 250150 Coordinates out of bounds (-1) Warning: Frame 257729 Coordinates out of bounds (-1) Warning: Frame 261811 Coordinates out of bounds (-1) Warning: Frame 266944 Coordinates out of bounds (-1) Warning: Frame 267701 Coordinates out of bounds (-1) Warning: Frame 270954 Coordinates out of bounds (-1) Warning: Frame 274456 Coordinates out of bounds (-1) Warning: Frame 274462 Coordinates out of bounds (-1) Warning: Frame 274892 Coordinates out of bounds (-1) Warning: Frame 281333 Coordinates out of bounds (-1) Warning: Frame 281348 Coordinates out of bounds (-1) Warning: Frame 282143 Coordinates out of bounds (-1) Warning: Frame 284108 Coordinates out of bounds (-1) Warning: Frame 284524 Coordinates out of bounds (-1) Warning: Frame 284542 Coordinates out of bounds (-1) Warning: Frame 288351 Coordinates out of bounds (-1) Warning: Frame 289199 Coordinates out of bounds (-1) Warning: Frame 289654 Coordinates out of bounds (-1) Warning: Frame 290870 Coordinates out of bounds (-1) Warning: Frame 290873 Coordinates out of bounds (-1) Warning: Frame 291377 Coordinates out of bounds (-1) Warning: Frame 292301 Coordinates out of bounds (-1) Warning: Frame 292507 Coordinates out of bounds (-1) Warning: Frame 293382 Coordinates out of bounds (-1) Warning: Frame 293533 Coordinates out of bounds (-1) Warning: Frame 294349 Coordinates out of bounds (-1) Warning: Frame 295474 Coordinates out of bounds (-1) Warning: Frame 296738 Coordinates out of bounds (-1) Warning: Frame 296921 Coordinates out of bounds (-1) Warning: Frame 297420 Coordinates out of bounds (-1) Warning: Frame 300199 Coordinates out of bounds (-1) Warning: Frame 300260 Coordinates out of bounds (-1) Warning: Frame 303363 Coordinates out of bounds (-1) Warning: Frame 304929 Coordinates out of bounds (-1) Warning: Frame 307343 Coordinates out of bounds (-1) Warning: Frame 308631 Coordinates out of bounds (-1) Warning: Frame 308931 Coordinates out of bounds (-1) Warning: Frame 309167 Coordinates out of bounds (-1) Warning: Frame 310657 Coordinates out of bounds (-1) Warning: Frame 310790 Coordinates out of bounds (-1) Warning: Frame 312900 Coordinates out of bounds (-1) Warning: Frame 313392 Coordinates out of bounds (-1) Warning: Frame 314021 Coordinates out of bounds (-1) Warning: Frame 314364 Coordinates out of bounds (-1) Warning: Frame 314546 Coordinates out of bounds (-1) Warning: Frame 315766 Coordinates out of bounds (-1) Warning: Frame 316499 Coordinates out of bounds (-1) Warning: Frame 316748 Coordinates out of bounds (-1) Warning: Frame 316749 Coordinates out of bounds (-1) Warning: Frame 317342 Coordinates out of bounds (-1) Warning: Frame 317527 Coordinates out of bounds (-1) Warning: Frame 320626 Coordinates out of bounds (-1) Warning: Frame 321166 Coordinates out of bounds (-1) Warning: Frame 322158 Coordinates out of bounds (-1) Warning: Frame 322554 Coordinates out of bounds (-1) Warning: Frame 324208 Coordinates out of bounds (-1) Warning: Frame 325084 Coordinates out of bounds (-1) Warning: Frame 325292 Coordinates out of bounds (-1) Warning: Frame 325952 Coordinates out of bounds (-1) Warning: Frame 326252 Coordinates out of bounds (-1) Warning: Frame 329712 Coordinates out of bounds (-1) Warning: Frame 335168 Coordinates out of bounds (-1) Warning: Frame 337692 Coordinates out of bounds (-1) Warning: Frame 338368 Coordinates out of bounds (-1) Warning: Frame 339244 Coordinates out of bounds (-1) Warning: Frame 343850 Coordinates out of bounds (-1) Warning: Frame 346262 Coordinates out of bounds (-1) Warning: Frame 346866 Coordinates out of bounds (-1) Warning: Frame 349692 Coordinates out of bounds (-1) Warning: Frame 355467 Coordinates out of bounds (-1) Warning: Frame 355951 Coordinates out of bounds (-1) Warning: Frame 356795 Coordinates out of bounds (-1) Warning: Frame 365454 Coordinates out of bounds (-1) Warning: Frame 373113 Coordinates out of bounds (-1) Warning: Frame 373136 Coordinates out of bounds (-1) Warning: Frame 376414 Coordinates out of bounds (-1) Warning: Frame 379485 Coordinates out of bounds (-1) Warning: Frame 386298 Coordinates out of bounds (-1) Warning: Frame 386365 Coordinates out of bounds (-1) Warning: Frame 400987 Coordinates out of bounds (-1) Warning: Frame 401333 Coordinates out of bounds (-1) Warning: Frame 403728 Coordinates out of bounds (-1) Warning: Frame 405030 Coordinates out of bounds (-1) Warning: Frame 405299 Coordinates out of bounds (-1) Warning: Frame 411905 Coordinates out of bounds (-1) Warning: Frame 417228 Coordinates out of bounds (-1) Warning: Frame 420150 Coordinates out of bounds (-1) Warning: Frame 421506 Coordinates out of bounds (-1) Warning: Frame 426101 Coordinates out of bounds (-1) Warning: Frame 434177 Coordinates out of bounds (-1) Warning: Frame 439604 Coordinates out of bounds (-1) Warning: Frame 441188 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Coordinates out of bounds (-1) Warning: Frame 1046711 Coordinates out of bounds (-1) Warning: Frame 1047596 Coordinates out of bounds (-1) Warning: Frame 1049906 Coordinates out of bounds (-1) Warning: Frame 1050370 Coordinates out of bounds (-1) Warning: Frame 1050988 Coordinates out of bounds (-1) Warning: Frame 1051063 Coordinates out of bounds (-1) Warning: Frame 1051339 Coordinates out of bounds (-1) Warning: Frame 1052360 Coordinates out of bounds (-1) Warning: Frame 1053266 Coordinates out of bounds (-1) Warning: Frame 1054854 Coordinates out of bounds (-1) Warning: Frame 1054855 Coordinates out of bounds (-1) Warning: Frame 1054974 Coordinates out of bounds (-1) Warning: Frame 1054982 Coordinates out of bounds (-1) Warning: Frame 1055227 Coordinates out of bounds (-1) Warning: Frame 1056078 Coordinates out of bounds (-1) Warning: Frame 1057143 Coordinates out of bounds (-1) Warning: Frame 1057411 Coordinates out of bounds (-1) Warning: Frame 1057679 Coordinates out of bounds (-1) Warning: Frame 1058356 Coordinates out of bounds (-1) Warning: Frame 1058800 Coordinates out of bounds (-1) Warning: Frame 1059002 Coordinates out of bounds (-1) Warning: Frame 1059175 Coordinates out of bounds (-1) Warning: Frame 1059176 Coordinates out of bounds (-1) Warning: Frame 1060262 Coordinates out of bounds (-1) Warning: Frame 1061145 Coordinates out of bounds (-1) Warning: Frame 1061442 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 1.06083e+06 2: [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: 1061716 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 1.06172e+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: 1061716 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 1.06172e+06 TIME: Analyses took 0.0964 seconds. DATASETS (10 total): dist2 "dist2" (double, distance), size is 1061716 d1 "d1" (double, torsion(delta)), size is 1061716 d2 "d2" (double, torsion(delta)), size is 1061716 e1 "e1" (double, torsion(epsilon)), size is 1061716 z1 "z1" (double, torsion(zeta)), size is 1061716 a2 "a2" (double, torsion(alpha)), size is 1061716 Hist_00022 "Hist_00022" (double matrix), size is 432000 Hist_00023 "Hist_00023" (double matrix), size is 432000 Hist_00024 "Hist_00024" (double matrix), size is 518400 Hist_00025 "Hist_00025" (double matrix), size is 518400 DATAFILES (4 total): 2dhist_e1_dist2.gnu (Gnuplot File): Hist_00022 2dhist_z1_dist2.gnu (Gnuplot File): Hist_00023 2dhist_z1_a2.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 : 1.0753 s ( 21.66%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0964 s ( 1.94%) TIME: Data File Write : 3.7921 s ( 76.39%) TIME: Other : 0.0006 s ( 0.00%) TIME: Run Total 4.9643 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 7.2848 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.