CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/21/16 12:29:25 | Available memory: 3.247 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.c3 parm [apa]] Reading '../../aa/cluster-all/km-7/ctraj.c3' as Amber NetCDF [trajin ../../ag/cluster-all/km-6/ctraj.c3 parm [apg]] Reading '../../ag/cluster-all/km-6/ctraj.c3' as Amber NetCDF [trajin ../../ag/cluster-all/km-6/ctraj.c4 parm [apg]] Reading '../../ag/cluster-all/km-6/ctraj.c4' as Amber NetCDF [trajin ../../ga/cluster-1-1/km-5/ctraj.c3 parm [gpa]] Reading '../../ga/cluster-1-1/km-5/ctraj.c3' as Amber NetCDF [trajin ../../gg/cluster-all/km-6/ctraj.c3 parm [gpg]] Reading '../../gg/cluster-all/km-6/ctraj.c3' as Amber NetCDF [trajin ../../ac/cluster-all/km-7/ctraj.c5 parm [apc]] Reading '../../ac/cluster-all/km-7/ctraj.c5' as Amber NetCDF [trajin ../../au/cluster-1-1/km-5/ctraj.c4 parm [apu]] Reading '../../au/cluster-1-1/km-5/ctraj.c4' as Amber NetCDF [trajin ../../gc/cluster-1-1/km-6-bbC2/ctraj.c4 parm [gpc]] Reading '../../gc/cluster-1-1/km-6-bbC2/ctraj.c4' as Amber NetCDF [trajin ../../gu/cluster-1-1/km-6/ctraj.c4 parm [gpu]] Reading '../../gu/cluster-1-1/km-6/ctraj.c4' as Amber NetCDF [trajin ../../ca/cluster-all/km-6/ctraj.c2 parm [cpa]] Reading '../../ca/cluster-all/km-6/ctraj.c2' as Amber NetCDF [trajin ../../cg/cluster-1-1/km-6-bbC2/ctraj.c2 parm [cpg]] Reading '../../cg/cluster-1-1/km-6-bbC2/ctraj.c2' as Amber NetCDF [trajin ../../ua/cluster-1-1/km-7/ctraj.c1 parm [upa]] Reading '../../ua/cluster-1-1/km-7/ctraj.c1' as Amber NetCDF [trajin ../../ug/cluster-1-1/km-6/ctraj.c1 parm [upg]] Reading '../../ug/cluster-1-1/km-6/ctraj.c1' as Amber NetCDF [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 (13 total): 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 50960 of 50960) 1: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 71210 of 71210) 2: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 47954 of 47954) 3: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7174 of 7174) 4: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 47410 of 47410) 5: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 43245 of 43245) 6: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 9975 of 9975) 7: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4050 of 4050) 8: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4722 of 4722) 9: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 88741 of 88741) 10: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 17719 of 17719) 11: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18590 of 18590) 12: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 19072 of 19072) Coordinate processing will occur on 430822 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (5 actions): 0: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 1: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 2: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 3: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 4: [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 (1-50960, 1) ----- 0% 10% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (5 actions): 0: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 1: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 2: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 3: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 4: [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 (1-71210, 1) ----- 20% ----- ctraj.c4 (1-47954, 1) ----- 30% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (5 actions): 0: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 1: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 2: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 3: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 4: [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 (1-7174, 1) ----- 40% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (5 actions): 0: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 1: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 2: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 3: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 4: [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 (1-47410, 1) ----- 50% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (5 actions): 0: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 1: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 2: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 3: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 4: [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.c5 (1-43245, 1) ----- 60% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (5 actions): 0: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 1: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 2: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 3: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 4: [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 (1-9975, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (5 actions): 0: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 1: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 2: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 3: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 4: [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 (1-4050, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (5 actions): 0: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 1: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 2: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 3: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 4: [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 (1-4722, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (5 actions): 0: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 1: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 2: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 3: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 4: [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 (1-88741, 1) ----- 70% 80% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (5 actions): 0: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 1: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 2: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 3: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 4: [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 (1-17719, 1) ----- 90% ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (5 actions): 0: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 1: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 2: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 3: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 4: [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 (1-18590, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (5 actions): 0: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 1: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 2: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 3: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 4: [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 (1-19072, 1) ----- 100% Complete. Read 430822 frames and processed 430822 frames. TIME: Avg. throughput= 328667.7810 frames / second. ACTION OUTPUT: DATASETS (5 total): d1 "d1" (double, torsion(delta)), size is 430822 d2 "d2" (double, torsion(delta)), size is 430822 e1 "e1" (double, torsion(epsilon)), size is 430822 z1 "z1" (double, torsion(zeta)), size is 430822 a2 "a2" (double, torsion(alpha)), size is 430822 RUN TIMING: TIME: Init : 0.0016 s ( 0.13%) TIME: Trajectory Process : 1.3108 s ( 99.87%) 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 1.3125 s ---------- RUN END --------------------------------------------------- [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 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. ---------- 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 (13 total): 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 50960 of 50960) 1: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 71210 of 71210) 2: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 47954 of 47954) 3: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7174 of 7174) 4: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 47410 of 47410) 5: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 43245 of 43245) 6: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 9975 of 9975) 7: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4050 of 4050) 8: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4722 of 4722) 9: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 88741 of 88741) 10: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 17719 of 17719) 11: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18590 of 18590) 12: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 19072 of 19072) Coordinate processing will occur on 430822 frames. BEGIN TRAJECTORY PROCESSING: ----- ctraj.c3 (1-50960, 1) ----- 0% 10% ----- ctraj.c3 (1-71210, 1) ----- 20% ----- ctraj.c4 (1-47954, 1) ----- 30% ----- ctraj.c3 (1-7174, 1) ----- 40% ----- ctraj.c3 (1-47410, 1) ----- 50% ----- ctraj.c5 (1-43245, 1) ----- 60% ----- ctraj.c4 (1-9975, 1) ----- ----- ctraj.c4 (1-4050, 1) ----- ----- ctraj.c4 (1-4722, 1) ----- ----- ctraj.c2 (1-88741, 1) ----- 70% 80% ----- ctraj.c2 (1-17719, 1) ----- 90% ----- ctraj.c1 (1-18590, 1) ----- ----- ctraj.c1 (1-19072, 1) ----- 100% Complete. Read 430822 frames and processed 430822 frames. TIME: Avg. throughput= 950318.1903 frames / second. ACTION OUTPUT: ANALYSIS: Performing 2 analyses: 0: [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: 430822 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 430822 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: 430822 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 430822 TIME: Analyses took 0.0237 seconds. DATASETS (7 total): d1 "d1" (double, torsion(delta)), size is 430822 d2 "d2" (double, torsion(delta)), size is 430822 e1 "e1" (double, torsion(epsilon)), size is 430822 z1 "z1" (double, torsion(zeta)), size is 430822 a2 "a2" (double, torsion(alpha)), size is 430822 Hist_00021 "Hist_00021" (double matrix), size is 518400 Hist_00022 "Hist_00022" (double matrix), size is 518400 DATAFILES (2 total): 2dhist_e1_d1.gnu (Gnuplot File): Hist_00021 2dhist_z1_a2.gnu (Gnuplot File): Hist_00022 RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 0.4533 s ( 20.49%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0237 s ( 1.07%) TIME: Data File Write : 1.7351 s ( 78.42%) TIME: Other : 0.0003 s ( 0.00%) TIME: Run Total 2.2124 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 3.6455 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.