CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 13:04:43 | Available memory: 1.547 GB INPUT: Reading input from 'pt-analysis.chi-pu.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.c0 parm [apa]] Reading '../../aa/cluster-all/km-7/ctraj.c0' as Amber NetCDF [trajin ../../aa/cluster-all/km-7/ctraj.c1 parm [apa]] Reading '../../aa/cluster-all/km-7/ctraj.c1' as Amber NetCDF [trajin ../../aa/cluster-all/km-7/ctraj.c2 parm [apa]] Reading '../../aa/cluster-all/km-7/ctraj.c2' as Amber NetCDF [trajin ../../aa/cluster-all/km-7/ctraj.c3 parm [apa]] Reading '../../aa/cluster-all/km-7/ctraj.c3' as Amber NetCDF [trajin ../../aa/cluster-all/km-7/ctraj.c4 parm [apa]] Reading '../../aa/cluster-all/km-7/ctraj.c4' as Amber NetCDF [trajin ../../aa/cluster-all/km-7/ctraj.c5 parm [apa]] Reading '../../aa/cluster-all/km-7/ctraj.c5' as Amber NetCDF [trajin ../../aa/cluster-all/km-7/ctraj.c6 parm [apa]] Reading '../../aa/cluster-all/km-7/ctraj.c6' 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 ../../ag/cluster-all/km-6/ctraj.c1 parm [apg]] Reading '../../ag/cluster-all/km-6/ctraj.c1' 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 ../../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 ../../ag/cluster-all/km-6/ctraj.c5 parm [apg]] Reading '../../ag/cluster-all/km-6/ctraj.c5' 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 ../../ga/cluster-1-1/km-5/ctraj.c1 parm [gpa]] Reading '../../ga/cluster-1-1/km-5/ctraj.c1' as Amber NetCDF [trajin ../../ga/cluster-1-1/km-5/ctraj.c2 parm [gpa]] Reading '../../ga/cluster-1-1/km-5/ctraj.c2' 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 ../../ga/cluster-1-1/km-5/ctraj.c4 parm [gpa]] Reading '../../ga/cluster-1-1/km-5/ctraj.c4' 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 ../../gg/cluster-all/km-6/ctraj.c1 parm [gpg]] Reading '../../gg/cluster-all/km-6/ctraj.c1' as Amber NetCDF [trajin ../../gg/cluster-all/km-6/ctraj.c2 parm [gpg]] Reading '../../gg/cluster-all/km-6/ctraj.c2' 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 ../../gg/cluster-all/km-6/ctraj.c4 parm [gpg]] Reading '../../gg/cluster-all/km-6/ctraj.c4' as Amber NetCDF [trajin ../../gg/cluster-all/km-6/ctraj.c5 parm [gpg]] Reading '../../gg/cluster-all/km-6/ctraj.c5' 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 ../../ac/cluster-all/km-7/ctraj.c1 parm [apc]] Reading '../../ac/cluster-all/km-7/ctraj.c1' as Amber NetCDF [trajin ../../ac/cluster-all/km-7/ctraj.c2 parm [apc]] Reading '../../ac/cluster-all/km-7/ctraj.c2' as Amber NetCDF [trajin ../../ac/cluster-all/km-7/ctraj.c3 parm [apc]] Reading '../../ac/cluster-all/km-7/ctraj.c3' as Amber NetCDF [trajin ../../ac/cluster-all/km-7/ctraj.c4 parm [apc]] Reading '../../ac/cluster-all/km-7/ctraj.c4' 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 ../../ac/cluster-all/km-7/ctraj.c6 parm [apc]] Reading '../../ac/cluster-all/km-7/ctraj.c6' 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 ../../au/cluster-1-1/km-5/ctraj.c1 parm [apu]] Reading '../../au/cluster-1-1/km-5/ctraj.c1' as Amber NetCDF [trajin ../../au/cluster-1-1/km-5/ctraj.c2 parm [apu]] Reading '../../au/cluster-1-1/km-5/ctraj.c2' as Amber NetCDF [trajin ../../au/cluster-1-1/km-5/ctraj.c3 parm [apu]] Reading '../../au/cluster-1-1/km-5/ctraj.c3' 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.c0 parm [gpc]] Reading '../../gc/cluster-1-1/km-6-bbC2/ctraj.c0' 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 ../../gc/cluster-1-1/km-6-bbC2/ctraj.c2 parm [gpc]] Reading '../../gc/cluster-1-1/km-6-bbC2/ctraj.c2' as Amber NetCDF [trajin ../../gc/cluster-1-1/km-6-bbC2/ctraj.c3 parm [gpc]] Reading '../../gc/cluster-1-1/km-6-bbC2/ctraj.c3' 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 ../../gc/cluster-1-1/km-6-bbC2/ctraj.c5 parm [gpc]] Reading '../../gc/cluster-1-1/km-6-bbC2/ctraj.c5' 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 ../../gu/cluster-1-1/km-6/ctraj.c1 parm [gpu]] Reading '../../gu/cluster-1-1/km-6/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 ../../gu/cluster-1-1/km-6/ctraj.c3 parm [gpu]] Reading '../../gu/cluster-1-1/km-6/ctraj.c3' 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 ../../gu/cluster-1-1/km-6/ctraj.c5 parm [gpu]] Reading '../../gu/cluster-1-1/km-6/ctraj.c5' as Amber NetCDF [distance dist3 :1@HO5' :1@N3] DISTANCE: :1@HO5' to :1@N3, center of mass. [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N9]-[:1@C4] 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 (48 total): 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 174638 of 174638) 1: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 164404 of 164404) 2: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 111938 of 111938) 3: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 50960 of 50960) 4: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 35573 of 35573) 5: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 35207 of 35207) 6: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 27280 of 27280) 7: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 228792 of 228792) 8: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 106435 of 106435) 9: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 99258 of 99258) 10: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 71210 of 71210) 11: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 47954 of 47954) 12: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 44686 of 44686) 13: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 34167 of 34167) 14: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 31448 of 31448) 15: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 23764 of 23764) 16: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7174 of 7174) 17: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3447 of 3447) 18: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 203546 of 203546) 19: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 189697 of 189697) 20: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 105190 of 105190) 21: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 47410 of 47410) 22: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 26755 of 26755) 23: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 23622 of 23622) 24: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 230147 of 230147) 25: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 109439 of 109439) 26: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 85717 of 85717) 27: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 49141 of 49141) 28: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 49129 of 49129) 29: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 43245 of 43245) 30: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 32915 of 32915) 31: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 41061 of 41061) 32: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 19943 of 19943) 33: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 17514 of 17514) 34: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 11507 of 11507) 35: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 9975 of 9975) 36: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 47347 of 47347) 37: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 24389 of 24389) 38: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 17259 of 17259) 39: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4174 of 4174) 40: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4050 of 4050) 41: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 2781 of 2781) 42: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 56497 of 56497) 43: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 17391 of 17391) 44: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 12720 of 12720) 45: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 5948 of 5948) 46: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4722 of 4722) 47: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 2722 of 2722) Coordinate processing will occur on 2794288 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [distance dist3 :1@HO5' :1@N3] :1@HO5' (1 atoms) to :1@N3 (1 atoms), imaged. 1: [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) ----- ctraj.c0 (1-174638, 1) ----- 0% ----- ctraj.c1 (1-164404, 1) ----- 10% ----- ctraj.c2 (1-111938, 1) ----- ----- ctraj.c3 (1-50960, 1) ----- ----- ctraj.c4 (1-35573, 1) ----- ----- ctraj.c5 (1-35207, 1) ----- 20% ----- ctraj.c6 (1-27280, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [distance dist3 :1@HO5' :1@N3] :1@HO5' (1 atoms) to :1@N3 (1 atoms), imaged. 1: [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) ----- ctraj.c0 (1-228792, 1) ----- ----- ctraj.c1 (1-106435, 1) ----- 30% ----- ctraj.c2 (1-99258, 1) ----- ----- ctraj.c3 (1-71210, 1) ----- ----- ctraj.c4 (1-47954, 1) ----- 40% ----- ctraj.c5 (1-44686, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [distance dist3 :1@HO5' :1@N3] :1@HO5' (1 atoms) to :1@N3 (1 atoms), imaged. 1: [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) ----- ctraj.c0 (1-34167, 1) ----- ----- ctraj.c1 (1-31448, 1) ----- ----- ctraj.c2 (1-23764, 1) ----- ----- ctraj.c3 (1-7174, 1) ----- ----- ctraj.c4 (1-3447, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [distance dist3 :1@HO5' :1@N3] :1@HO5' (1 atoms) to :1@N3 (1 atoms), imaged. 1: [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) ----- ctraj.c0 (1-203546, 1) ----- 50% ----- ctraj.c1 (1-189697, 1) ----- 60% ----- ctraj.c2 (1-105190, 1) ----- ----- ctraj.c3 (1-47410, 1) ----- ----- ctraj.c4 (1-26755, 1) ----- ----- ctraj.c5 (1-23622, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [distance dist3 :1@HO5' :1@N3] :1@HO5' (1 atoms) to :1@N3 (1 atoms), imaged. 1: [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) ----- ctraj.c0 (1-230147, 1) ----- 70% ----- ctraj.c1 (1-109439, 1) ----- ----- ctraj.c2 (1-85717, 1) ----- 80% ----- ctraj.c3 (1-49141, 1) ----- ----- ctraj.c4 (1-49129, 1) ----- ----- ctraj.c5 (1-43245, 1) ----- ----- ctraj.c6 (1-32915, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [distance dist3 :1@HO5' :1@N3] :1@HO5' (1 atoms) to :1@N3 (1 atoms), imaged. 1: [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) ----- ctraj.c0 (1-41061, 1) ----- 90% ----- ctraj.c1 (1-19943, 1) ----- ----- ctraj.c2 (1-17514, 1) ----- ----- ctraj.c3 (1-11507, 1) ----- ----- ctraj.c4 (1-9975, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [distance dist3 :1@HO5' :1@N3] :1@HO5' (1 atoms) to :1@N3 (1 atoms), imaged. 1: [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) ----- ctraj.c0 (1-47347, 1) ----- ----- ctraj.c1 (1-24389, 1) ----- ----- ctraj.c2 (1-17259, 1) ----- ----- ctraj.c3 (1-4174, 1) ----- ----- ctraj.c4 (1-4050, 1) ----- ----- ctraj.c5 (1-2781, 1) ----- ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (2 actions): 0: [distance dist3 :1@HO5' :1@N3] :1@HO5' (1 atoms) to :1@N3 (1 atoms), imaged. 1: [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chi] [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) ----- ctraj.c0 (1-56497, 1) ----- ----- ctraj.c1 (1-17391, 1) ----- ----- ctraj.c2 (1-12720, 1) ----- ----- ctraj.c3 (1-5948, 1) ----- ----- ctraj.c4 (1-4722, 1) ----- ----- ctraj.c5 (1-2722, 1) ----- 100% Complete. Read 2794288 frames and processed 2794288 frames. TIME: Avg. throughput= 680156.4247 frames / second. ACTION OUTPUT: DATASETS (2 total): dist3 "dist3" (double, distance), size is 2794288 c1 "c1" (double, torsion(chin)), size is 2794288 RUN TIMING: TIME: Init : 0.0005 s ( 0.01%) TIME: Trajectory Process : 4.1083 s ( 99.99%) 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 4.1088 s ---------- RUN END --------------------------------------------------- [hist c1,-180,180,0.5 dist3,0,10,0.01 out 2dhist_c1_dist3-pu.gnu norm] Hist: 2dhist_c1_dist3-pu.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 (48 total): 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 174638 of 174638) 1: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 164404 of 164404) 2: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 111938 of 111938) 3: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 50960 of 50960) 4: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 35573 of 35573) 5: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 35207 of 35207) 6: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 27280 of 27280) 7: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 228792 of 228792) 8: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 106435 of 106435) 9: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 99258 of 99258) 10: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 71210 of 71210) 11: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 47954 of 47954) 12: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 44686 of 44686) 13: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 34167 of 34167) 14: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 31448 of 31448) 15: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 23764 of 23764) 16: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 7174 of 7174) 17: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 3447 of 3447) 18: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 203546 of 203546) 19: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 189697 of 189697) 20: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 105190 of 105190) 21: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 47410 of 47410) 22: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 26755 of 26755) 23: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 23622 of 23622) 24: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 230147 of 230147) 25: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 109439 of 109439) 26: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 85717 of 85717) 27: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 49141 of 49141) 28: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 49129 of 49129) 29: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 43245 of 43245) 30: 'ctraj.c6' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 32915 of 32915) 31: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 41061 of 41061) 32: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 19943 of 19943) 33: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 17514 of 17514) 34: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 11507 of 11507) 35: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 9975 of 9975) 36: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 47347 of 47347) 37: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 24389 of 24389) 38: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 17259 of 17259) 39: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4174 of 4174) 40: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4050 of 4050) 41: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 2781 of 2781) 42: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 56497 of 56497) 43: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 17391 of 17391) 44: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 12720 of 12720) 45: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 5948 of 5948) 46: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 4722 of 4722) 47: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 2722 of 2722) Coordinate processing will occur on 2794288 frames. BEGIN TRAJECTORY PROCESSING: ----- ctraj.c0 (1-174638, 1) ----- 0% ----- ctraj.c1 (1-164404, 1) ----- 10% ----- ctraj.c2 (1-111938, 1) ----- ----- ctraj.c3 (1-50960, 1) ----- ----- ctraj.c4 (1-35573, 1) ----- ----- ctraj.c5 (1-35207, 1) ----- 20% ----- ctraj.c6 (1-27280, 1) ----- ----- ctraj.c0 (1-228792, 1) ----- ----- ctraj.c1 (1-106435, 1) ----- 30% ----- ctraj.c2 (1-99258, 1) ----- ----- ctraj.c3 (1-71210, 1) ----- ----- ctraj.c4 (1-47954, 1) ----- 40% ----- ctraj.c5 (1-44686, 1) ----- ----- ctraj.c0 (1-34167, 1) ----- ----- ctraj.c1 (1-31448, 1) ----- ----- ctraj.c2 (1-23764, 1) ----- ----- ctraj.c3 (1-7174, 1) ----- ----- ctraj.c4 (1-3447, 1) ----- ----- ctraj.c0 (1-203546, 1) ----- 50% ----- ctraj.c1 (1-189697, 1) ----- 60% ----- ctraj.c2 (1-105190, 1) ----- ----- ctraj.c3 (1-47410, 1) ----- ----- ctraj.c4 (1-26755, 1) ----- ----- ctraj.c5 (1-23622, 1) ----- ----- ctraj.c0 (1-230147, 1) ----- 70% ----- ctraj.c1 (1-109439, 1) ----- ----- ctraj.c2 (1-85717, 1) ----- 80% ----- ctraj.c3 (1-49141, 1) ----- ----- ctraj.c4 (1-49129, 1) ----- ----- ctraj.c5 (1-43245, 1) ----- ----- ctraj.c6 (1-32915, 1) ----- ----- ctraj.c0 (1-41061, 1) ----- 90% ----- ctraj.c1 (1-19943, 1) ----- ----- ctraj.c2 (1-17514, 1) ----- ----- ctraj.c3 (1-11507, 1) ----- ----- ctraj.c4 (1-9975, 1) ----- ----- ctraj.c0 (1-47347, 1) ----- ----- ctraj.c1 (1-24389, 1) ----- ----- ctraj.c2 (1-17259, 1) ----- ----- ctraj.c3 (1-4174, 1) ----- ----- ctraj.c4 (1-4050, 1) ----- ----- ctraj.c5 (1-2781, 1) ----- ----- ctraj.c0 (1-56497, 1) ----- ----- ctraj.c1 (1-17391, 1) ----- ----- ctraj.c2 (1-12720, 1) ----- ----- ctraj.c3 (1-5948, 1) ----- ----- ctraj.c4 (1-4722, 1) ----- ----- ctraj.c5 (1-2722, 1) ----- 100% Complete. Read 2794288 frames and processed 2794288 frames. TIME: Avg. throughput= 985740.6880 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [hist c1,-180,180,0.5 dist3,0,10,0.01 out 2dhist_c1_dist3-pu.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: 2794288 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 2.79429e+06 TIME: Analyses took 0.0645 seconds. DATASETS (3 total): dist3 "dist3" (double, distance), size is 2794288 c1 "c1" (double, torsion(chin)), size is 2794288 Hist_00018 "Hist_00018" (double matrix), size is 720000 DATAFILES (1 total): 2dhist_c1_dist3-pu.gnu (Gnuplot File): Hist_00018 RUN TIMING: TIME: Init : 0.0001 s ( 0.00%) TIME: Trajectory Process : 2.8347 s ( 71.92%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0645 s ( 1.64%) TIME: Data File Write : 1.0421 s ( 26.44%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 3.9416 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 8.3286 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.