CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 13:05:03 | Available memory: 1.634 GB INPUT: Reading input from 'pt-analysis.chi-py.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 ../../ca/cluster-all/km-6/ctraj.c0 parm [cpa]] Reading '../../ca/cluster-all/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 ../../ca/cluster-all/km-6/ctraj.c2 parm [cpa]] Reading '../../ca/cluster-all/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 ../../ca/cluster-all/km-6/ctraj.c4 parm [cpa]] Reading '../../ca/cluster-all/km-6/ctraj.c4' as Amber NetCDF [trajin ../../ca/cluster-all/km-6/ctraj.c5 parm [cpa]] Reading '../../ca/cluster-all/km-6/ctraj.c5' 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 ../../cg/cluster-1-1/km-6-bbC2/ctraj.c1 parm [cpg]] Reading '../../cg/cluster-1-1/km-6-bbC2/ctraj.c1' 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 ../../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 ../../cg/cluster-1-1/km-6-bbC2/ctraj.c4 parm [cpg]] Reading '../../cg/cluster-1-1/km-6-bbC2/ctraj.c4' as Amber NetCDF [trajin ../../cg/cluster-1-1/km-6-bbC2/ctraj.c5 parm [cpg]] Reading '../../cg/cluster-1-1/km-6-bbC2/ctraj.c5' 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 ../../ua/cluster-1-1/km-7/ctraj.c1 parm [upa]] Reading '../../ua/cluster-1-1/km-7/ctraj.c1' as Amber NetCDF [trajin ../../ua/cluster-1-1/km-7/ctraj.c2 parm [upa]] Reading '../../ua/cluster-1-1/km-7/ctraj.c2' 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 ../../ua/cluster-1-1/km-7/ctraj.c4 parm [upa]] Reading '../../ua/cluster-1-1/km-7/ctraj.c4' as Amber NetCDF [trajin ../../ua/cluster-1-1/km-7/ctraj.c5 parm [upa]] Reading '../../ua/cluster-1-1/km-7/ctraj.c5' as Amber NetCDF [trajin ../../ua/cluster-1-1/km-7/ctraj.c6 parm [upa]] Reading '../../ua/cluster-1-1/km-7/ctraj.c6' 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 ../../ug/cluster-1-1/km-6/ctraj.c1 parm [upg]] Reading '../../ug/cluster-1-1/km-6/ctraj.c1' as Amber NetCDF [trajin ../../ug/cluster-1-1/km-6/ctraj.c2 parm [upg]] Reading '../../ug/cluster-1-1/km-6/ctraj.c2' 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 ../../ug/cluster-1-1/km-6/ctraj.c4 parm [upg]] Reading '../../ug/cluster-1-1/km-6/ctraj.c4' as Amber NetCDF [trajin ../../ug/cluster-1-1/km-6/ctraj.c5 parm [upg]] Reading '../../ug/cluster-1-1/km-6/ctraj.c5' 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 ../../cc/cluster-all/km-5/ctraj.c1 parm [cpc]] Reading '../../cc/cluster-all/km-5/ctraj.c1' as Amber NetCDF [trajin ../../cc/cluster-all/km-5/ctraj.c2 parm [cpc]] Reading '../../cc/cluster-all/km-5/ctraj.c2' 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 ../../cc/cluster-all/km-5/ctraj.c4 parm [cpc]] Reading '../../cc/cluster-all/km-5/ctraj.c4' 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 ../../cu/cluster-1-1/km-5-bbC2/ctraj.c1 parm [cpu]] Reading '../../cu/cluster-1-1/km-5-bbC2/ctraj.c1' as Amber NetCDF [trajin ../../cu/cluster-1-1/km-5-bbC2/ctraj.c2 parm [cpu]] Reading '../../cu/cluster-1-1/km-5-bbC2/ctraj.c2' as Amber NetCDF [trajin ../../cu/cluster-1-1/km-5-bbC2/ctraj.c3 parm [cpu]] Reading '../../cu/cluster-1-1/km-5-bbC2/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.c0 parm [upc]] Reading '../../uc/cluster-1-1/km-5/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 ../../uc/cluster-1-1/km-5/ctraj.c2 parm [upc]] Reading '../../uc/cluster-1-1/km-5/ctraj.c2' 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 ../../uc/cluster-1-1/km-5/ctraj.c4 parm [upc]] Reading '../../uc/cluster-1-1/km-5/ctraj.c4' as Amber NetCDF [trajin ../../uu/cluster-all/km-5/ctraj.c0 parm [upu]] Reading '../../uu/cluster-all/km-5/ctraj.c0' as Amber NetCDF [trajin ../../uu/cluster-all/km-5/ctraj.c1 parm [upu]] Reading '../../uu/cluster-all/km-5/ctraj.c1' as Amber NetCDF [trajin ../../uu/cluster-all/km-5/ctraj.c2 parm [upu]] Reading '../../uu/cluster-all/km-5/ctraj.c2' as Amber NetCDF [trajin ../../uu/cluster-all/km-5/ctraj.c3 parm [upu]] Reading '../../uu/cluster-all/km-5/ctraj.c3' as Amber NetCDF [trajin ../../uu/cluster-all/km-5/ctraj.c4 parm [upu]] Reading '../../uu/cluster-all/km-5/ctraj.c4' as Amber NetCDF [distance dist3 :1@HO5' :1@O2] DISTANCE: :1@HO5' to :1@O2, center of mass. [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi] DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N1]-[:1@C2] 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 (45 total): 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 172040 of 172040) 1: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 145142 of 145142) 2: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 88741 of 88741) 3: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 77630 of 77630) 4: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 74884 of 74884) 5: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 41559 of 41559) 6: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 40201 of 40201) 7: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 21662 of 21662) 8: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 17719 of 17719) 9: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 12023 of 12023) 10: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4545 of 4545) 11: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3850 of 3850) 12: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 50866 of 50866) 13: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18590 of 18590) 14: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 13501 of 13501) 15: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 6487 of 6487) 16: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4720 of 4720) 17: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3875 of 3875) 18: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 1961 of 1961) 19: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 49458 of 49458) 20: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 19072 of 19072) 21: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18784 of 18784) 22: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 5656 of 5656) 23: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3855 of 3855) 24: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3175 of 3175) 25: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 273041 of 273041) 26: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 134387 of 134387) 27: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 76671 of 76671) 28: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 67544 of 67544) 29: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 48280 of 48280) 30: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 55868 of 55868) 31: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18571 of 18571) 32: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 10292 of 10292) 33: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7787 of 7787) 34: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7482 of 7482) 35: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 36137 of 36137) 36: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 27062 of 27062) 37: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 15117 of 15117) 38: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 11047 of 11047) 39: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 10637 of 10637) 40: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 225909 of 225909) 41: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 126351 of 126351) 42: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 90296 of 90296) 43: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 86746 of 86746) 44: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 68322 of 68322) Coordinate processing will occur on 2297543 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [distance dist3 :1@HO5' :1@O2] :1@HO5' (1 atoms) to :1@O2 (1 atoms), imaged. 1: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1) ----- ctraj.c0 (1-172040, 1) ----- 0% ----- ctraj.c1 (1-145142, 1) ----- 10% ----- ctraj.c2 (1-88741, 1) ----- ----- ctraj.c3 (1-77630, 1) ----- 20% ----- ctraj.c4 (1-74884, 1) ----- ----- ctraj.c5 (1-41559, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [distance dist3 :1@HO5' :1@O2] :1@HO5' (1 atoms) to :1@O2 (1 atoms), imaged. 1: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1) ----- ctraj.c0 (1-40201, 1) ----- ----- ctraj.c1 (1-21662, 1) ----- ----- ctraj.c2 (1-17719, 1) ----- ----- ctraj.c3 (1-12023, 1) ----- 30% ----- ctraj.c4 (1-4545, 1) ----- ----- ctraj.c5 (1-3850, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [distance dist3 :1@HO5' :1@O2] :1@HO5' (1 atoms) to :1@O2 (1 atoms), imaged. 1: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1) ----- ctraj.c0 (1-50866, 1) ----- ----- ctraj.c1 (1-18590, 1) ----- ----- ctraj.c2 (1-13501, 1) ----- ----- ctraj.c3 (1-6487, 1) ----- ----- ctraj.c4 (1-4720, 1) ----- ----- ctraj.c5 (1-3875, 1) ----- ----- ctraj.c6 (1-1961, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [distance dist3 :1@HO5' :1@O2] :1@HO5' (1 atoms) to :1@O2 (1 atoms), imaged. 1: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1) ----- ctraj.c0 (1-49458, 1) ----- ----- ctraj.c1 (1-19072, 1) ----- ----- ctraj.c2 (1-18784, 1) ----- ----- ctraj.c3 (1-5656, 1) ----- ----- ctraj.c4 (1-3855, 1) ----- ----- ctraj.c5 (1-3175, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [distance dist3 :1@HO5' :1@O2] :1@HO5' (1 atoms) to :1@O2 (1 atoms), imaged. 1: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1) ----- ctraj.c0 (1-273041, 1) ----- 40% 50% ----- ctraj.c1 (1-134387, 1) ----- ----- ctraj.c2 (1-76671, 1) ----- 60% ----- ctraj.c3 (1-67544, 1) ----- ----- ctraj.c4 (1-48280, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [distance dist3 :1@HO5' :1@O2] :1@HO5' (1 atoms) to :1@O2 (1 atoms), imaged. 1: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1) ----- ctraj.c0 (1-55868, 1) ----- ----- ctraj.c1 (1-18571, 1) ----- ----- ctraj.c2 (1-10292, 1) ----- ----- ctraj.c3 (1-7787, 1) ----- ----- ctraj.c4 (1-7482, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [distance dist3 :1@HO5' :1@O2] :1@HO5' (1 atoms) to :1@O2 (1 atoms), imaged. 1: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1) ----- ctraj.c0 (1-36137, 1) ----- 70% ----- ctraj.c1 (1-27062, 1) ----- ----- ctraj.c2 (1-15117, 1) ----- ----- ctraj.c3 (1-11047, 1) ----- ----- ctraj.c4 (1-10637, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [distance dist3 :1@HO5' :1@O2] :1@HO5' (1 atoms) to :1@O2 (1 atoms), imaged. 1: [dihedral c1 :1@O4' :1@C1' :1@N1 :1@C2 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N1](1) [:1@C2](1) ----- ctraj.c0 (1-225909, 1) ----- 80% ----- ctraj.c1 (1-126351, 1) ----- ----- ctraj.c2 (1-90296, 1) ----- 90% ----- ctraj.c3 (1-86746, 1) ----- ----- ctraj.c4 (1-68322, 1) ----- 100% Complete. Read 2297543 frames and processed 2297543 frames. TIME: Avg. throughput= 681686.0280 frames / second. ACTION OUTPUT: DATASETS (2 total): dist3 "dist3" (double, distance), size is 2297543 c1 "c1" (double, torsion(chin)), size is 2297543 RUN TIMING: TIME: Init : 0.0005 s ( 0.01%) TIME: Trajectory Process : 3.3704 s ( 99.98%) 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 3.3709 s ---------- RUN END --------------------------------------------------- [hist c1,-180,180,0.5 dist3,0,10,0.01 out 2dhist_c1_dist3-py.gnu norm] Hist: 2dhist_c1_dist3-py.gnu: Set up for 2 dimensions using the following datasets: [ c1 dist3 ] 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 (45 total): 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 172040 of 172040) 1: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 145142 of 145142) 2: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 88741 of 88741) 3: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 77630 of 77630) 4: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 74884 of 74884) 5: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 41559 of 41559) 6: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 40201 of 40201) 7: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 21662 of 21662) 8: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 17719 of 17719) 9: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 12023 of 12023) 10: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4545 of 4545) 11: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3850 of 3850) 12: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 50866 of 50866) 13: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18590 of 18590) 14: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 13501 of 13501) 15: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 6487 of 6487) 16: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4720 of 4720) 17: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3875 of 3875) 18: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 1961 of 1961) 19: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 49458 of 49458) 20: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 19072 of 19072) 21: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18784 of 18784) 22: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 5656 of 5656) 23: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3855 of 3855) 24: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3175 of 3175) 25: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 273041 of 273041) 26: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 134387 of 134387) 27: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 76671 of 76671) 28: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 67544 of 67544) 29: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 48280 of 48280) 30: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 55868 of 55868) 31: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18571 of 18571) 32: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 10292 of 10292) 33: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7787 of 7787) 34: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7482 of 7482) 35: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 36137 of 36137) 36: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 27062 of 27062) 37: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 15117 of 15117) 38: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 11047 of 11047) 39: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 10637 of 10637) 40: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 225909 of 225909) 41: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 126351 of 126351) 42: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 90296 of 90296) 43: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 86746 of 86746) 44: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 68322 of 68322) Coordinate processing will occur on 2297543 frames. BEGIN TRAJECTORY PROCESSING: ----- ctraj.c0 (1-172040, 1) ----- 0% ----- ctraj.c1 (1-145142, 1) ----- 10% ----- ctraj.c2 (1-88741, 1) ----- ----- ctraj.c3 (1-77630, 1) ----- 20% ----- ctraj.c4 (1-74884, 1) ----- ----- ctraj.c5 (1-41559, 1) ----- ----- ctraj.c0 (1-40201, 1) ----- ----- ctraj.c1 (1-21662, 1) ----- ----- ctraj.c2 (1-17719, 1) ----- ----- ctraj.c3 (1-12023, 1) ----- 30% ----- ctraj.c4 (1-4545, 1) ----- ----- ctraj.c5 (1-3850, 1) ----- ----- ctraj.c0 (1-50866, 1) ----- ----- ctraj.c1 (1-18590, 1) ----- ----- ctraj.c2 (1-13501, 1) ----- ----- ctraj.c3 (1-6487, 1) ----- ----- ctraj.c4 (1-4720, 1) ----- ----- ctraj.c5 (1-3875, 1) ----- ----- ctraj.c6 (1-1961, 1) ----- ----- ctraj.c0 (1-49458, 1) ----- ----- ctraj.c1 (1-19072, 1) ----- ----- ctraj.c2 (1-18784, 1) ----- ----- ctraj.c3 (1-5656, 1) ----- ----- ctraj.c4 (1-3855, 1) ----- ----- ctraj.c5 (1-3175, 1) ----- ----- ctraj.c0 (1-273041, 1) ----- 40% 50% ----- ctraj.c1 (1-134387, 1) ----- ----- ctraj.c2 (1-76671, 1) ----- 60% ----- ctraj.c3 (1-67544, 1) ----- ----- ctraj.c4 (1-48280, 1) ----- ----- ctraj.c0 (1-55868, 1) ----- ----- ctraj.c1 (1-18571, 1) ----- ----- ctraj.c2 (1-10292, 1) ----- ----- ctraj.c3 (1-7787, 1) ----- ----- ctraj.c4 (1-7482, 1) ----- ----- ctraj.c0 (1-36137, 1) ----- 70% ----- ctraj.c1 (1-27062, 1) ----- ----- ctraj.c2 (1-15117, 1) ----- ----- ctraj.c3 (1-11047, 1) ----- ----- ctraj.c4 (1-10637, 1) ----- ----- ctraj.c0 (1-225909, 1) ----- 80% ----- ctraj.c1 (1-126351, 1) ----- ----- ctraj.c2 (1-90296, 1) ----- 90% ----- ctraj.c3 (1-86746, 1) ----- ----- ctraj.c4 (1-68322, 1) ----- 100% Complete. Read 2297543 frames and processed 2297543 frames. TIME: Avg. throughput= 1023207.5610 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [hist c1,-180,180,0.5 dist3,0,10,0.01 out 2dhist_c1_dist3-py.gnu norm] Calculating bins from min=-180 max=180 step=0.5. Dim c1: -180.000000->180.000000, step 0.500000, 720 bins. Calculating bins from min=0 max=10 step=0.01. Dim dist3: 0.000000->10.000000, step 0.010000, 1000 bins. Hist: 2297543 data points in each dimension. Hist: Allocating histogram, total bins = 720000 Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 2.29754e+06 TIME: Analyses took 0.0526 seconds. DATASETS (3 total): dist3 "dist3" (double, distance), size is 2297543 c1 "c1" (double, torsion(chin)), size is 2297543 Hist_00018 "Hist_00018" (double matrix), size is 720000 DATAFILES (1 total): 2dhist_c1_dist3-py.gnu (Gnuplot File): Hist_00018 RUN TIMING: TIME: Init : 0.0001 s ( 0.00%) TIME: Trajectory Process : 2.2454 s ( 67.25%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0526 s ( 1.58%) TIME: Data File Write : 1.0406 s ( 31.17%) TIME: Other : 0.0002 s ( 0.00%) TIME: Run Total 3.3389 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 6.9617 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.