CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/04/15 14:07:52 | Available memory: 15354.2 MB INPUT: Reading Input from file pt-clust.in [parm ../../tip3p/ff12sb/run1/build/full.topo.hmr [tip3p-ff12sb]] Reading '../../tip3p/ff12sb/run1/build/full.topo.hmr' as Amber Topology [parm ../../tip3p/dacP-ff12sb/run1/build/full.topo.hmr [tip3p-dacP-ff12sb]] Reading '../../tip3p/dacP-ff12sb/run1/build/full.topo.hmr' as Amber Topology [parm ../../tip3p/chen-garcia/run1/build/full.topo.hmr [tip3p-chen-garcia]] Reading '../../tip3p/chen-garcia/run1/build/full.topo.hmr' as Amber Topology [parm ../../tip3p/charmm36/run1/build/full.topo.hmr [tip3p-charmm36]] Reading '../../tip3p/charmm36/run1/build/full.topo.hmr' as Amber Topology CHAMBER topology: 1: CHARMM 361 * \\\\ CHARMM36 All-Hydrogen Nucleic Acid Topology File /// [parm ../../opc/ff12sb/run1/build/full.topo.hmr [opc-ff12sb]] Reading '../../opc/ff12sb/run1/build/full.topo.hmr' as Amber Topology [parm ../../opc/dacP-ff12sb/run1/build/full.topo.hmr [opc-dacP-ff12sb]] Reading '../../opc/dacP-ff12sb/run1/build/full.topo.hmr' as Amber Topology [trajin ../../tip3p/ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/ff12sb/run1/traj.1.02,../../tip3p/ff12sb/run1/traj.1.03,../../tip3p/ff12sb/run1/traj.1.04,../../tip3p/ff12sb/run1/traj.1.05,../../tip3p/ff12sb/run1/traj.1.06,../../tip3p/ff12sb/run1/traj.1.07,../../tip3p/ff12sb/run1/traj.1.08,../../tip3p/ff12sb/run1/traj.1.09,../../tip3p/ff12sb/run1/traj.1.10,../../tip3p/ff12sb/run1/traj.1.11,../../tip3p/ff12sb/run1/traj.1.12,../../tip3p/ff12sb/run1/traj.1.13,../../tip3p/ff12sb/run1/traj.1.14,../../tip3p/ff12sb/run1/traj.1.15,../../tip3p/ff12sb/run1/traj.1.16,../../tip3p/ff12sb/run1/traj.1.17,../../tip3p/ff12sb/run1/traj.1.18 parm [tip3p-ff12sb]] Reading '../../tip3p/ff12sb/run1/traj.1.01' as Amber NetCDF Reading '../../tip3p/ff12sb/run1/traj.1.02' as Amber NetCDF Reading '../../tip3p/ff12sb/run1/traj.1.03' as Amber NetCDF Reading '../../tip3p/ff12sb/run1/traj.1.04' as Amber NetCDF Reading '../../tip3p/ff12sb/run1/traj.1.05' as Amber NetCDF Reading '../../tip3p/ff12sb/run1/traj.1.06' as Amber NetCDF Reading '../../tip3p/ff12sb/run1/traj.1.07' as Amber NetCDF Reading '../../tip3p/ff12sb/run1/traj.1.08' as Amber NetCDF Reading '../../tip3p/ff12sb/run1/traj.1.09' as Amber NetCDF Reading '../../tip3p/ff12sb/run1/traj.1.10' as Amber NetCDF Reading '../../tip3p/ff12sb/run1/traj.1.11' as Amber NetCDF Reading '../../tip3p/ff12sb/run1/traj.1.12' as Amber NetCDF Reading '../../tip3p/ff12sb/run1/traj.1.13' as Amber NetCDF Reading '../../tip3p/ff12sb/run1/traj.1.14' as Amber NetCDF Reading '../../tip3p/ff12sb/run1/traj.1.15' as Amber NetCDF Reading '../../tip3p/ff12sb/run1/traj.1.16' as Amber NetCDF Reading '../../tip3p/ff12sb/run1/traj.1.17' as Amber NetCDF Reading '../../tip3p/ff12sb/run1/traj.1.18' as Amber NetCDF [trajin ../../tip3p/ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/ff12sb/run2/traj.1.02,../../tip3p/ff12sb/run2/traj.1.03,../../tip3p/ff12sb/run2/traj.1.04,../../tip3p/ff12sb/run2/traj.1.05,../../tip3p/ff12sb/run2/traj.1.06,../../tip3p/ff12sb/run2/traj.1.07,../../tip3p/ff12sb/run2/traj.1.08,../../tip3p/ff12sb/run2/traj.1.09,../../tip3p/ff12sb/run2/traj.1.10,../../tip3p/ff12sb/run2/traj.1.11,../../tip3p/ff12sb/run2/traj.1.12,../../tip3p/ff12sb/run2/traj.1.13,../../tip3p/ff12sb/run2/traj.1.14,../../tip3p/ff12sb/run2/traj.1.15,../../tip3p/ff12sb/run2/traj.1.16,../../tip3p/ff12sb/run2/traj.1.17,../../tip3p/ff12sb/run2/traj.1.18 parm [tip3p-ff12sb]] Reading '../../tip3p/ff12sb/run2/traj.1.01' as Amber NetCDF Reading '../../tip3p/ff12sb/run2/traj.1.02' as Amber NetCDF Reading '../../tip3p/ff12sb/run2/traj.1.03' as Amber NetCDF Reading '../../tip3p/ff12sb/run2/traj.1.04' as Amber NetCDF Reading '../../tip3p/ff12sb/run2/traj.1.05' as Amber NetCDF Reading '../../tip3p/ff12sb/run2/traj.1.06' as Amber NetCDF Reading '../../tip3p/ff12sb/run2/traj.1.07' as Amber NetCDF Reading '../../tip3p/ff12sb/run2/traj.1.08' as Amber NetCDF Reading '../../tip3p/ff12sb/run2/traj.1.09' as Amber NetCDF Reading '../../tip3p/ff12sb/run2/traj.1.10' as Amber NetCDF Reading '../../tip3p/ff12sb/run2/traj.1.11' as Amber NetCDF Reading '../../tip3p/ff12sb/run2/traj.1.12' as Amber NetCDF Reading '../../tip3p/ff12sb/run2/traj.1.13' as Amber NetCDF Reading '../../tip3p/ff12sb/run2/traj.1.14' as Amber NetCDF Reading '../../tip3p/ff12sb/run2/traj.1.15' as Amber NetCDF Reading '../../tip3p/ff12sb/run2/traj.1.16' as Amber NetCDF Reading '../../tip3p/ff12sb/run2/traj.1.17' as Amber NetCDF Reading '../../tip3p/ff12sb/run2/traj.1.18' as Amber NetCDF [trajin ../../tip3p/dacP-ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/dacP-ff12sb/run1/traj.1.02,../../tip3p/dacP-ff12sb/run1/traj.1.03,../../tip3p/dacP-ff12sb/run1/traj.1.04,../../tip3p/dacP-ff12sb/run1/traj.1.05,../../tip3p/dacP-ff12sb/run1/traj.1.06,../../tip3p/dacP-ff12sb/run1/traj.1.07,../../tip3p/dacP-ff12sb/run1/traj.1.08,../../tip3p/dacP-ff12sb/run1/traj.1.09,../../tip3p/dacP-ff12sb/run1/traj.1.10,../../tip3p/dacP-ff12sb/run1/traj.1.11,../../tip3p/dacP-ff12sb/run1/traj.1.12,../../tip3p/dacP-ff12sb/run1/traj.1.13,../../tip3p/dacP-ff12sb/run1/traj.1.14,../../tip3p/dacP-ff12sb/run1/traj.1.15,../../tip3p/dacP-ff12sb/run1/traj.1.16,../../tip3p/dacP-ff12sb/run1/traj.1.17,../../tip3p/dacP-ff12sb/run1/traj.1.18 parm [tip3p-dacP-ff12sb]] Reading '../../tip3p/dacP-ff12sb/run1/traj.1.01' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run1/traj.1.02' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run1/traj.1.03' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run1/traj.1.04' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run1/traj.1.05' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run1/traj.1.06' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run1/traj.1.07' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run1/traj.1.08' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run1/traj.1.09' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run1/traj.1.10' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run1/traj.1.11' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run1/traj.1.12' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run1/traj.1.13' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run1/traj.1.14' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run1/traj.1.15' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run1/traj.1.16' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run1/traj.1.17' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run1/traj.1.18' as Amber NetCDF [trajin ../../tip3p/dacP-ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/dacP-ff12sb/run2/traj.1.02,../../tip3p/dacP-ff12sb/run2/traj.1.03,../../tip3p/dacP-ff12sb/run2/traj.1.04,../../tip3p/dacP-ff12sb/run2/traj.1.05,../../tip3p/dacP-ff12sb/run2/traj.1.06,../../tip3p/dacP-ff12sb/run2/traj.1.07,../../tip3p/dacP-ff12sb/run2/traj.1.08,../../tip3p/dacP-ff12sb/run2/traj.1.09,../../tip3p/dacP-ff12sb/run2/traj.1.10,../../tip3p/dacP-ff12sb/run2/traj.1.11,../../tip3p/dacP-ff12sb/run2/traj.1.12,../../tip3p/dacP-ff12sb/run2/traj.1.13,../../tip3p/dacP-ff12sb/run2/traj.1.14,../../tip3p/dacP-ff12sb/run2/traj.1.15,../../tip3p/dacP-ff12sb/run2/traj.1.16,../../tip3p/dacP-ff12sb/run2/traj.1.17,../../tip3p/dacP-ff12sb/run2/traj.1.18 parm [tip3p-dacP-ff12sb] ] Reading '../../tip3p/dacP-ff12sb/run2/traj.1.01' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run2/traj.1.02' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run2/traj.1.03' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run2/traj.1.04' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run2/traj.1.05' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run2/traj.1.06' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run2/traj.1.07' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run2/traj.1.08' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run2/traj.1.09' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run2/traj.1.10' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run2/traj.1.11' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run2/traj.1.12' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run2/traj.1.13' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run2/traj.1.14' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run2/traj.1.15' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run2/traj.1.16' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run2/traj.1.17' as Amber NetCDF Reading '../../tip3p/dacP-ff12sb/run2/traj.1.18' as Amber NetCDF [trajin ../../tip3p/chen-garcia/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/chen-garcia/run1/traj.1.02,../../tip3p/chen-garcia/run1/traj.1.03,../../tip3p/chen-garcia/run1/traj.1.04,../../tip3p/chen-garcia/run1/traj.1.05,../../tip3p/chen-garcia/run1/traj.1.06,../../tip3p/chen-garcia/run1/traj.1.07,../../tip3p/chen-garcia/run1/traj.1.08,../../tip3p/chen-garcia/run1/traj.1.09,../../tip3p/chen-garcia/run1/traj.1.10,../../tip3p/chen-garcia/run1/traj.1.11,../../tip3p/chen-garcia/run1/traj.1.12,../../tip3p/chen-garcia/run1/traj.1.13,../../tip3p/chen-garcia/run1/traj.1.14,../../tip3p/chen-garcia/run1/traj.1.15,../../tip3p/chen-garcia/run1/traj.1.16,../../tip3p/chen-garcia/run1/traj.1.17,../../tip3p/chen-garcia/run1/traj.1.18 parm [tip3p-chen-garcia]] Reading '../../tip3p/chen-garcia/run1/traj.1.01' as Amber NetCDF Reading '../../tip3p/chen-garcia/run1/traj.1.02' as Amber NetCDF Reading '../../tip3p/chen-garcia/run1/traj.1.03' as Amber NetCDF Reading '../../tip3p/chen-garcia/run1/traj.1.04' as Amber NetCDF Reading '../../tip3p/chen-garcia/run1/traj.1.05' as Amber NetCDF Reading '../../tip3p/chen-garcia/run1/traj.1.06' as Amber NetCDF Reading '../../tip3p/chen-garcia/run1/traj.1.07' as Amber NetCDF Reading '../../tip3p/chen-garcia/run1/traj.1.08' as Amber NetCDF Reading '../../tip3p/chen-garcia/run1/traj.1.09' as Amber NetCDF Reading '../../tip3p/chen-garcia/run1/traj.1.10' as Amber NetCDF Reading '../../tip3p/chen-garcia/run1/traj.1.11' as Amber NetCDF Reading '../../tip3p/chen-garcia/run1/traj.1.12' as Amber NetCDF Reading '../../tip3p/chen-garcia/run1/traj.1.13' as Amber NetCDF Reading '../../tip3p/chen-garcia/run1/traj.1.14' as Amber NetCDF Reading '../../tip3p/chen-garcia/run1/traj.1.15' as Amber NetCDF Reading '../../tip3p/chen-garcia/run1/traj.1.16' as Amber NetCDF Reading '../../tip3p/chen-garcia/run1/traj.1.17' as Amber NetCDF Reading '../../tip3p/chen-garcia/run1/traj.1.18' as Amber NetCDF [trajin ../../tip3p/chen-garcia/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/chen-garcia/run2/traj.1.02,../../tip3p/chen-garcia/run2/traj.1.03,../../tip3p/chen-garcia/run2/traj.1.04,../../tip3p/chen-garcia/run2/traj.1.05,../../tip3p/chen-garcia/run2/traj.1.06,../../tip3p/chen-garcia/run2/traj.1.07,../../tip3p/chen-garcia/run2/traj.1.08,../../tip3p/chen-garcia/run2/traj.1.09,../../tip3p/chen-garcia/run2/traj.1.10,../../tip3p/chen-garcia/run2/traj.1.11,../../tip3p/chen-garcia/run2/traj.1.12,../../tip3p/chen-garcia/run2/traj.1.13,../../tip3p/chen-garcia/run2/traj.1.14,../../tip3p/chen-garcia/run2/traj.1.15,../../tip3p/chen-garcia/run2/traj.1.16,../../tip3p/chen-garcia/run2/traj.1.17,../../tip3p/chen-garcia/run2/traj.1.18 parm [tip3p-chen-garcia]] Reading '../../tip3p/chen-garcia/run2/traj.1.01' as Amber NetCDF Reading '../../tip3p/chen-garcia/run2/traj.1.02' as Amber NetCDF Reading '../../tip3p/chen-garcia/run2/traj.1.03' as Amber NetCDF Reading '../../tip3p/chen-garcia/run2/traj.1.04' as Amber NetCDF Reading '../../tip3p/chen-garcia/run2/traj.1.05' as Amber NetCDF Reading '../../tip3p/chen-garcia/run2/traj.1.06' as Amber NetCDF Reading '../../tip3p/chen-garcia/run2/traj.1.07' as Amber NetCDF Reading '../../tip3p/chen-garcia/run2/traj.1.08' as Amber NetCDF Reading '../../tip3p/chen-garcia/run2/traj.1.09' as Amber NetCDF Reading '../../tip3p/chen-garcia/run2/traj.1.10' as Amber NetCDF Reading '../../tip3p/chen-garcia/run2/traj.1.11' as Amber NetCDF Reading '../../tip3p/chen-garcia/run2/traj.1.12' as Amber NetCDF Reading '../../tip3p/chen-garcia/run2/traj.1.13' as Amber NetCDF Reading '../../tip3p/chen-garcia/run2/traj.1.14' as Amber NetCDF Reading '../../tip3p/chen-garcia/run2/traj.1.15' as Amber NetCDF Reading '../../tip3p/chen-garcia/run2/traj.1.16' as Amber NetCDF Reading '../../tip3p/chen-garcia/run2/traj.1.17' as Amber NetCDF Reading '../../tip3p/chen-garcia/run2/traj.1.18' as Amber NetCDF [trajin ../../tip3p/charmm36/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/charmm36/run1/traj.1.02,../../tip3p/charmm36/run1/traj.1.03,../../tip3p/charmm36/run1/traj.1.04,../../tip3p/charmm36/run1/traj.1.05,../../tip3p/charmm36/run1/traj.1.06,../../tip3p/charmm36/run1/traj.1.07,../../tip3p/charmm36/run1/traj.1.08,../../tip3p/charmm36/run1/traj.1.09,../../tip3p/charmm36/run1/traj.1.10,../../tip3p/charmm36/run1/traj.1.11,../../tip3p/charmm36/run1/traj.1.12,../../tip3p/charmm36/run1/traj.1.13,../../tip3p/charmm36/run1/traj.1.14,../../tip3p/charmm36/run1/traj.1.15,../../tip3p/charmm36/run1/traj.1.16,../../tip3p/charmm36/run1/traj.1.17,../../tip3p/charmm36/run1/traj.1.18 parm [tip3p-charmm36]] Reading '../../tip3p/charmm36/run1/traj.1.01' as Amber NetCDF Reading '../../tip3p/charmm36/run1/traj.1.02' as Amber NetCDF Reading '../../tip3p/charmm36/run1/traj.1.03' as Amber NetCDF Reading '../../tip3p/charmm36/run1/traj.1.04' as Amber NetCDF Reading '../../tip3p/charmm36/run1/traj.1.05' as Amber NetCDF Reading '../../tip3p/charmm36/run1/traj.1.06' as Amber NetCDF Reading '../../tip3p/charmm36/run1/traj.1.07' as Amber NetCDF Reading '../../tip3p/charmm36/run1/traj.1.08' as Amber NetCDF Reading '../../tip3p/charmm36/run1/traj.1.09' as Amber NetCDF Reading '../../tip3p/charmm36/run1/traj.1.10' as Amber NetCDF Reading '../../tip3p/charmm36/run1/traj.1.11' as Amber NetCDF Reading '../../tip3p/charmm36/run1/traj.1.12' as Amber NetCDF Reading '../../tip3p/charmm36/run1/traj.1.13' as Amber NetCDF Reading '../../tip3p/charmm36/run1/traj.1.14' as Amber NetCDF Reading '../../tip3p/charmm36/run1/traj.1.15' as Amber NetCDF Reading '../../tip3p/charmm36/run1/traj.1.16' as Amber NetCDF Reading '../../tip3p/charmm36/run1/traj.1.17' as Amber NetCDF Reading '../../tip3p/charmm36/run1/traj.1.18' as Amber NetCDF [trajin ../../tip3p/charmm36/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/charmm36/run2/traj.1.02,../../tip3p/charmm36/run2/traj.1.03,../../tip3p/charmm36/run2/traj.1.04,../../tip3p/charmm36/run2/traj.1.05,../../tip3p/charmm36/run2/traj.1.06,../../tip3p/charmm36/run2/traj.1.07,../../tip3p/charmm36/run2/traj.1.08,../../tip3p/charmm36/run2/traj.1.09,../../tip3p/charmm36/run2/traj.1.10,../../tip3p/charmm36/run2/traj.1.11,../../tip3p/charmm36/run2/traj.1.12,../../tip3p/charmm36/run2/traj.1.13,../../tip3p/charmm36/run2/traj.1.14,../../tip3p/charmm36/run2/traj.1.15,../../tip3p/charmm36/run2/traj.1.16,../../tip3p/charmm36/run2/traj.1.17,../../tip3p/charmm36/run2/traj.1.18 parm [tip3p-charmm36]] Reading '../../tip3p/charmm36/run2/traj.1.01' as Amber NetCDF Reading '../../tip3p/charmm36/run2/traj.1.02' as Amber NetCDF Reading '../../tip3p/charmm36/run2/traj.1.03' as Amber NetCDF Reading '../../tip3p/charmm36/run2/traj.1.04' as Amber NetCDF Reading '../../tip3p/charmm36/run2/traj.1.05' as Amber NetCDF Reading '../../tip3p/charmm36/run2/traj.1.06' as Amber NetCDF Reading '../../tip3p/charmm36/run2/traj.1.07' as Amber NetCDF Reading '../../tip3p/charmm36/run2/traj.1.08' as Amber NetCDF Reading '../../tip3p/charmm36/run2/traj.1.09' as Amber NetCDF Reading '../../tip3p/charmm36/run2/traj.1.10' as Amber NetCDF Reading '../../tip3p/charmm36/run2/traj.1.11' as Amber NetCDF Reading '../../tip3p/charmm36/run2/traj.1.12' as Amber NetCDF Reading '../../tip3p/charmm36/run2/traj.1.13' as Amber NetCDF Reading '../../tip3p/charmm36/run2/traj.1.14' as Amber NetCDF Reading '../../tip3p/charmm36/run2/traj.1.15' as Amber NetCDF Reading '../../tip3p/charmm36/run2/traj.1.16' as Amber NetCDF Reading '../../tip3p/charmm36/run2/traj.1.17' as Amber NetCDF Reading '../../tip3p/charmm36/run2/traj.1.18' as Amber NetCDF [trajin ../../opc/ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../opc/ff12sb/run1/traj.1.02,../../opc/ff12sb/run1/traj.1.03,../../opc/ff12sb/run1/traj.1.04,../../opc/ff12sb/run1/traj.1.05,../../opc/ff12sb/run1/traj.1.06,../../opc/ff12sb/run1/traj.1.07,../../opc/ff12sb/run1/traj.1.08,../../opc/ff12sb/run1/traj.1.09,../../opc/ff12sb/run1/traj.1.10,../../opc/ff12sb/run1/traj.1.11,../../opc/ff12sb/run1/traj.1.12,../../opc/ff12sb/run1/traj.1.13,../../opc/ff12sb/run1/traj.1.14,../../opc/ff12sb/run1/traj.1.15,../../opc/ff12sb/run1/traj.1.16,../../opc/ff12sb/run1/traj.1.17,../../opc/ff12sb/run1/traj.1.18 parm [opc-ff12sb]] Reading '../../opc/ff12sb/run1/traj.1.01' as Amber NetCDF Reading '../../opc/ff12sb/run1/traj.1.02' as Amber NetCDF Reading '../../opc/ff12sb/run1/traj.1.03' as Amber NetCDF Reading '../../opc/ff12sb/run1/traj.1.04' as Amber NetCDF Reading '../../opc/ff12sb/run1/traj.1.05' as Amber NetCDF Reading '../../opc/ff12sb/run1/traj.1.06' as Amber NetCDF Reading '../../opc/ff12sb/run1/traj.1.07' as Amber NetCDF Reading '../../opc/ff12sb/run1/traj.1.08' as Amber NetCDF Reading '../../opc/ff12sb/run1/traj.1.09' as Amber NetCDF Reading '../../opc/ff12sb/run1/traj.1.10' as Amber NetCDF Reading '../../opc/ff12sb/run1/traj.1.11' as Amber NetCDF Reading '../../opc/ff12sb/run1/traj.1.12' as Amber NetCDF Reading '../../opc/ff12sb/run1/traj.1.13' as Amber NetCDF Reading '../../opc/ff12sb/run1/traj.1.14' as Amber NetCDF Reading '../../opc/ff12sb/run1/traj.1.15' as Amber NetCDF Reading '../../opc/ff12sb/run1/traj.1.16' as Amber NetCDF Reading '../../opc/ff12sb/run1/traj.1.17' as Amber NetCDF Reading '../../opc/ff12sb/run1/traj.1.18' as Amber NetCDF [trajin ../../opc/ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../opc/ff12sb/run2/traj.1.02,../../opc/ff12sb/run2/traj.1.03,../../opc/ff12sb/run2/traj.1.04,../../opc/ff12sb/run2/traj.1.05,../../opc/ff12sb/run2/traj.1.06,../../opc/ff12sb/run2/traj.1.07,../../opc/ff12sb/run2/traj.1.08,../../opc/ff12sb/run2/traj.1.09,../../opc/ff12sb/run2/traj.1.10,../../opc/ff12sb/run2/traj.1.11,../../opc/ff12sb/run2/traj.1.12,../../opc/ff12sb/run2/traj.1.13,../../opc/ff12sb/run2/traj.1.14,../../opc/ff12sb/run2/traj.1.15,../../opc/ff12sb/run2/traj.1.16,../../opc/ff12sb/run2/traj.1.17,../../opc/ff12sb/run2/traj.1.18 parm [opc-ff12sb]] Reading '../../opc/ff12sb/run2/traj.1.01' as Amber NetCDF Reading '../../opc/ff12sb/run2/traj.1.02' as Amber NetCDF Reading '../../opc/ff12sb/run2/traj.1.03' as Amber NetCDF Reading '../../opc/ff12sb/run2/traj.1.04' as Amber NetCDF Reading '../../opc/ff12sb/run2/traj.1.05' as Amber NetCDF Reading '../../opc/ff12sb/run2/traj.1.06' as Amber NetCDF Reading '../../opc/ff12sb/run2/traj.1.07' as Amber NetCDF Reading '../../opc/ff12sb/run2/traj.1.08' as Amber NetCDF Reading '../../opc/ff12sb/run2/traj.1.09' as Amber NetCDF Reading '../../opc/ff12sb/run2/traj.1.10' as Amber NetCDF Reading '../../opc/ff12sb/run2/traj.1.11' as Amber NetCDF Reading '../../opc/ff12sb/run2/traj.1.12' as Amber NetCDF Reading '../../opc/ff12sb/run2/traj.1.13' as Amber NetCDF Reading '../../opc/ff12sb/run2/traj.1.14' as Amber NetCDF Reading '../../opc/ff12sb/run2/traj.1.15' as Amber NetCDF Reading '../../opc/ff12sb/run2/traj.1.16' as Amber NetCDF Reading '../../opc/ff12sb/run2/traj.1.17' as Amber NetCDF Reading '../../opc/ff12sb/run2/traj.1.18' as Amber NetCDF [trajin ../../opc/dacP-ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../opc/dacP-ff12sb/run1/traj.1.02,../../opc/dacP-ff12sb/run1/traj.1.03,../../opc/dacP-ff12sb/run1/traj.1.04,../../opc/dacP-ff12sb/run1/traj.1.05,../../opc/dacP-ff12sb/run1/traj.1.06,../../opc/dacP-ff12sb/run1/traj.1.07,../../opc/dacP-ff12sb/run1/traj.1.08,../../opc/dacP-ff12sb/run1/traj.1.09,../../opc/dacP-ff12sb/run1/traj.1.10,../../opc/dacP-ff12sb/run1/traj.1.11,../../opc/dacP-ff12sb/run1/traj.1.12,../../opc/dacP-ff12sb/run1/traj.1.13,../../opc/dacP-ff12sb/run1/traj.1.14,../../opc/dacP-ff12sb/run1/traj.1.15,../../opc/dacP-ff12sb/run1/traj.1.16,../../opc/dacP-ff12sb/run1/traj.1.17,../../opc/dacP-ff12sb/run1/traj.1.18 parm [opc-dacP-ff12sb]] Reading '../../opc/dacP-ff12sb/run1/traj.1.01' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run1/traj.1.02' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run1/traj.1.03' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run1/traj.1.04' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run1/traj.1.05' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run1/traj.1.06' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run1/traj.1.07' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run1/traj.1.08' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run1/traj.1.09' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run1/traj.1.10' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run1/traj.1.11' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run1/traj.1.12' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run1/traj.1.13' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run1/traj.1.14' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run1/traj.1.15' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run1/traj.1.16' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run1/traj.1.17' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run1/traj.1.18' as Amber NetCDF [trajin ../../opc/dacP-ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../opc/dacP-ff12sb/run2/traj.1.02,../../opc/dacP-ff12sb/run2/traj.1.03,../../opc/dacP-ff12sb/run2/traj.1.04,../../opc/dacP-ff12sb/run2/traj.1.05,../../opc/dacP-ff12sb/run2/traj.1.06,../../opc/dacP-ff12sb/run2/traj.1.07,../../opc/dacP-ff12sb/run2/traj.1.08,../../opc/dacP-ff12sb/run2/traj.1.09,../../opc/dacP-ff12sb/run2/traj.1.10,../../opc/dacP-ff12sb/run2/traj.1.11,../../opc/dacP-ff12sb/run2/traj.1.12,../../opc/dacP-ff12sb/run2/traj.1.13,../../opc/dacP-ff12sb/run2/traj.1.14,../../opc/dacP-ff12sb/run2/traj.1.15,../../opc/dacP-ff12sb/run2/traj.1.16,../../opc/dacP-ff12sb/run2/traj.1.17,../../opc/dacP-ff12sb/run2/traj.1.18 parm [opc-dacP-ff12sb]] Reading '../../opc/dacP-ff12sb/run2/traj.1.01' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run2/traj.1.02' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run2/traj.1.03' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run2/traj.1.04' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run2/traj.1.05' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run2/traj.1.06' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run2/traj.1.07' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run2/traj.1.08' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run2/traj.1.09' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run2/traj.1.10' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run2/traj.1.11' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run2/traj.1.12' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run2/traj.1.13' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run2/traj.1.14' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run2/traj.1.15' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run2/traj.1.16' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run2/traj.1.17' as Amber NetCDF Reading '../../opc/dacP-ff12sb/run2/traj.1.18' as Amber NetCDF [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [strip :WAT,Na+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [rmsd :1-2&!@H= first mass out test.dat] RMSD: (:1-2&!@H*), reference is first frame (:1-2&!@H*), with fitting, mass-weighted. [cluster :1,2&!@H= summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 6 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000,150000,200000,250000,300000,350000,400000,448978,498386,547099,596220] CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:1,2&!@H=]) best-fit K-MEANS: Looking for 6 clusters. Sequentially modify each point. Cluster to cluster distance will be based on cluster centroids. Initial clustering will be randomly sieved (with value 200). Previously calcd pair distances CpptrajPairDist will be used if found. Summary of cluster results will be written to clust-summary.dat Summary comparing parts of trajectory data for clusters will be written to split.dat Frames will be split at: 50000 100000 150000 200000 250000 300000 350000 400000 448978 498386 547099 596220 Cluster trajectories will be written to ctraj, format Amber NetCDF Cluster representatives will be written to separate trajectories, prefix (rep), format PDB Warning: One or more analyses requested creation of default COORDS DataSet. CREATECRD: Saving coordinates from Top [tip3p-ff12sb] to "_DEFAULTCRD_" ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [tip3p-ff12sb] 'full.topo.hmr', 3303 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 100000 frames 1: [tip3p-dacP-ff12sb] 'full.topo.hmr', 3303 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 100000 frames 2: [tip3p-chen-garcia] 'full.topo.hmr', 3303 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 100000 frames 3: [tip3p-charmm36] 'full.topo.hmr', 3303 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 100000 frames 4: [opc-ff12sb] 'full.topo.hmr', 4378 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 98386 frames 5: [opc-dacP-ff12sb] 'full.topo.hmr', 4378 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 97834 frames INPUT TRAJECTORIES: 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 1: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 2: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 3: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 4: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 5: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 6: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 7: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 8: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 48978 of 48978) Looking for frames at 298.41 K 9: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 49408 of 49408) Looking for frames at 298.41 K 10: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 48713 of 48713) Looking for frames at 298.41 K 11: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 49121 of 49121) Looking for frames at 298.41 K Coordinate processing will occur on 596220 frames. TIME: Run Initialization took 0.0018 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[tip3p-ff12sb]' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 67 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass out test.dat] Target mask: [:1-2&!@H*](43) Reference mask: [:1-2&!@H*](43) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] Warning: COORDS data sets do not store temperatures. Warning: COORDS data sets do not store times. Estimated memory usage (100000 frames): 79 MB ----- traj.1.01 (1-50000, 1) ----- 0% REMD: OPENING 18 REMD TRAJECTORIES ----- traj.1.01 (1-50000, 1) ----- 10% REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[tip3p-dacP-ff12sb]' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 67 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass out test.dat] Target mask: [:1-2&!@H*](43) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] ----- traj.1.01 (1-50000, 1) ----- 20% REMD: OPENING 18 REMD TRAJECTORIES ----- traj.1.01 (1-50000, 1) ----- 30% REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[tip3p-chen-garcia]' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 67 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass out test.dat] Target mask: [:1-2&!@H*](43) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] ----- traj.1.01 (1-50000, 1) ----- 40% REMD: OPENING 18 REMD TRAJECTORIES ----- traj.1.01 (1-50000, 1) ----- 50% REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[tip3p-charmm36]' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 67 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass out test.dat] Target mask: [:1-2&!@H*](43) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] ----- traj.1.01 (1-50000, 1) ----- REMD: OPENING 18 REMD TRAJECTORIES ----- traj.1.01 (1-50000, 1) ----- 60% REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[opc-ff12sb]' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 4311 atoms. Stripped parm: 'full.topo.hmr', 67 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass out test.dat] Target mask: [:1-2&!@H*](43) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] ----- traj.1.01 (1-48978, 1) ----- 70% REMD: OPENING 18 REMD TRAJECTORIES ----- traj.1.01 (1-49408, 1) ----- 80% REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[opc-dacP-ff12sb]' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 4311 atoms. Stripped parm: 'full.topo.hmr', 67 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass out test.dat] Target mask: [:1-2&!@H*](43) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] ----- traj.1.01 (1-48713, 1) ----- 90% REMD: OPENING 18 REMD TRAJECTORIES ----- traj.1.01 (1-49121, 1) ----- 100% Complete. Read 596220 frames and processed 596220 frames. TIME: Trajectory processing: 6993.0467 s TIME: Avg. throughput= 85.2590 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [cluster :1,2&!@H= summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 6 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000,150000,200000,250000,300000,350000,400000,448978,498386,547099,596220] Starting clustering. Mask [:1,2&!@H*] corresponds to 43 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (1193450000) Estimated pair-wise matrix memory usage: > 16.9551 MB Pair-wise matrix set up with sieve, 596220 frames, 2982 sieved frames. 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete. Saving pair-wise distances to CpptrajPairDist Memory used by pair-wise matrix and other cluster data: 19.7982 MB Round 0: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 0: 2976 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 610 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 189 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 104 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 48 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 19 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 19 points changed cluster assignment. Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 7: 7 points changed cluster assignment. Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 8: 4 points changed cluster assignment. Round 9: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 9: 7 points changed cluster assignment. Round 10: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 10: 26 points changed cluster assignment. Round 11: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 11: 40 points changed cluster assignment. Round 12: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 12: 22 points changed cluster assignment. Round 13: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 13: 6 points changed cluster assignment. Round 14: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 14: 6 points changed cluster assignment. Round 15: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 15: 1 points changed cluster assignment. Round 16: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 16: No change. Skipping the rest of the iterations. Restoring sieved frames. Parallelizing calculation with 8 threads 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete. #Clustering: 6 clusters 596220 frames #Cluster 0 has average-distance-to-centroid 1.080196 #Cluster 1 has average-distance-to-centroid 1.258746 #Cluster 2 has average-distance-to-centroid 1.251148 #Cluster 3 has average-distance-to-centroid 1.661809 #Cluster 4 has average-distance-to-centroid 1.587530 #Cluster 5 has average-distance-to-centroid 2.003425 #DBI: 1.649023 #pSF: 131352.978020 #Algorithm: Kmeans nclusters 6 maxit 100 #Representative frames: 561210 325241 492145 134415 369686 213386 #Sieve value: 200 (random) #Sieved frames: 481 489 807 1033 1197 1431 1545 1905 1998 2363 2867 2881 3327 3671 3724 3731 4059 4363 5035 5068 5433 5461 6000 6032 6064 6598 6682 7084 7098 7347 7610 7703 7818 7967 8256 8409 8433 8776 8871 9022 9068 9322 9479 9546 9773 10182 10231 10550 10830 11038 11248 11387 11492 11526 11592 11961 11997 12018 12116 12219 12401 13031 13040 13149 13366 13429 14284 14297 14454 14643 14759 14897 15127 15163 15361 15431 15685 15766 15816 16048 16692 16744 16841 16859 17135 17437 17471 17606 17764 17989 18047 18360 18881 18954 19430 19976 20532 20614 20653 20729 21515 21649 21843 22412 22517 22620 22822 22845 23008 23172 23223 23228 23394 23513 23586 23649 23836 23960 24014 24106 24218 24514 24617 24738 24843 25070 26424 26505 26717 26853 27088 27145 27164 27234 27717 27852 27885 28341 28471 28490 29688 29833 30030 30046 30068 30083 30606 30727 30842 30947 30951 30999 31207 31306 31322 31838 31866 31946 32002 32065 32190 32340 32409 32435 32897 32917 32959 33462 33516 34210 35380 35385 35438 35516 35641 35851 35979 36052 36169 36173 36289 36317 36857 37076 37193 37352 37482 37587 37680 37846 37856 37871 37886 38058 38316 38548 38790 39153 39170 39245 39866 39891 40318 40364 40398 40413 40531 40554 40593 40812 40932 40944 41088 41202 41252 41348 41361 41505 41552 41579 41633 41674 41679 41966 41983 41994 42060 42127 42217 42272 42458 42479 42700 42708 42981 43159 43227 43368 43410 43416 43773 44049 44414 44458 44514 44571 44748 44813 44985 44998 45096 45235 45380 45552 46002 46082 46356 46733 46956 46958 47039 47587 48238 48239 48538 48684 49742 50127 50920 50996 51110 51320 51418 51485 51804 52582 52584 52804 52957 53297 53394 53547 53557 53726 53771 54240 54521 54740 54787 55134 55295 55327 55607 55608 55689 55824 55867 55998 56046 56106 56410 56480 56784 57001 57105 57750 57817 57848 58116 58371 58399 58853 58982 58984 59014 59470 59510 59672 59840 59899 60082 60818 60879 60891 61361 61655 61814 62460 63113 63143 63157 65081 65137 65166 65187 65393 65603 65940 66722 66886 67001 67138 67215 67716 68336 68368 68475 68815 69127 69177 69291 69395 69565 69805 69879 70014 70075 70327 70335 71107 71432 71510 71513 71562 71993 72000 72065 72228 72491 73399 74152 74355 74750 75078 75111 75228 75682 76079 76126 76189 76192 76308 76409 76825 76926 77020 77792 77951 78036 78279 78623 78683 79159 79307 79321 79657 79898 80219 80254 80368 80540 80721 81003 81852 81931 81957 81962 82120 82350 82924 83030 83319 84010 84150 84554 84915 85235 85237 85517 85578 85834 86036 86866 86963 87108 87500 87800 87852 87995 88300 88356 88671 89203 89376 89831 90113 90128 90376 90483 90580 90684 91134 91142 91434 91748 92257 92394 92548 92817 93349 93599 93639 93769 93783 94062 94151 94381 94414 94811 94956 95011 95167 95365 95444 95523 96078 96273 96345 96532 96944 97345 97377 97413 97504 97520 97743 97889 98014 98050 98061 98124 98136 98210 98347 98438 98658 98708 98869 99157 99239 99250 99334 99375 100026 100105 100381 100402 100666 100845 101350 102278 102388 102593 102735 102866 102930 102943 103045 103086 103129 103219 103333 103466 103685 103873 104029 104143 104556 104719 104756 104805 104850 104872 105589 106005 106031 106129 106304 106695 106827 106877 107337 107434 107842 107938 107940 108047 108664 108820 108866 108928 109462 109463 109483 109544 109760 109851 110013 110190 110317 110422 110779 110785 111043 112178 112218 112285 112292 112435 112484 112492 112519 112540 112674 112850 113100 113192 113912 114125 114349 114355 114394 114455 114484 114822 114923 116018 116170 116204 116276 116555 117169 117188 117551 117583 117957 118146 118172 118885 118935 119327 119552 119610 120277 120296 120684 121025 121467 121711 122010 122214 122250 122327 122368 122541 122943 123340 123500 123511 123521 123610 123746 123979 124089 124150 124193 124359 124445 124837 125151 125252 125306 125794 125874 125970 126381 126826 127061 127112 127285 127705 127760 127838 128207 128589 129132 129578 129885 130008 130050 130120 130206 130323 130397 130503 130885 130994 131005 131368 131385 131553 131628 131798 132158 132682 132799 132843 132998 133435 133440 133824 134010 134041 134415 134962 135215 135467 135652 135873 136234 136594 136688 137045 137580 138125 138219 138839 139162 139752 139770 140363 140509 140515 140548 140574 140782 141118 141301 141342 141497 141513 141860 142021 142263 142278 142325 142404 142438 142506 142569 142914 143076 143239 143429 143724 143753 143813 143905 144168 144259 144296 144823 145078 145099 145264 145273 145286 145333 145600 145609 145613 146212 146225 146522 146568 146626 147400 147462 147858 147896 148134 148756 148760 149013 149239 149496 149794 150154 150204 150318 150739 150895 151217 151320 151621 152250 152415 152458 152514 152539 152580 152629 152735 153103 153534 153925 154154 154341 154690 154724 154855 155194 155233 155536 155790 156548 156606 156780 156944 156983 158086 158632 158736 158855 158876 159164 159263 159278 159384 159697 159886 160721 160849 161075 161133 161197 161326 161570 161680 161745 161895 161911 162368 162458 162670 162744 162845 163758 163859 163967 164223 164721 165508 165611 165623 166453 166472 166688 166863 166977 167419 167628 167978 167987 168390 168636 168696 168892 168925 169738 169906 170058 170131 170474 170935 171143 172641 173330 174015 174494 175232 175934 176604 177286 177479 177657 177766 177836 178628 178654 178865 178904 178921 179113 179214 179606 179707 179910 179912 179989 180115 180368 180422 180441 180566 180998 181172 181219 181828 181918 182259 182276 182279 182388 182391 182770 182912 183051 183567 183650 184228 184288 184447 184630 184647 184695 184697 184712 184778 184849 185160 185220 185297 185345 185482 185556 185681 185800 185949 185957 186190 186322 186341 186650 186707 186765 186816 186847 186959 187205 187260 187516 187835 188132 188263 188515 188717 188721 189352 189371 189842 190093 190406 190679 191215 191309 191649 191650 191759 191764 191850 191881 191967 192009 192054 192608 192672 192862 192866 193068 193176 193238 193370 193600 193711 194362 194850 195004 195084 195147 195558 195847 196235 196257 196539 196594 196745 197937 197951 197953 197955 198177 198245 198503 198611 199012 199226 199540 200349 200451 201181 201334 201436 201553 201892 201944 203383 203533 203672 204209 204548 204700 204713 205005 205041 205455 205706 205933 206667 206725 206780 206844 207193 208363 208604 208800 208833 209044 209168 209187 209220 209359 209453 209529 209971 210234 210255 210610 210629 210799 211372 212215 212477 212713 212806 212834 212991 213010 213191 213386 213731 214164 214404 214720 214739 214862 215110 215879 216181 216197 216204 216258 216746 216944 217088 217339 217556 217797 217814 217928 218167 218381 218662 219467 219474 219556 219799 219914 220030 220157 220527 220640 220771 220929 220944 221089 221113 221362 221432 221461 221501 221551 221852 222677 222825 223231 223298 223367 223549 223796 223800 223932 224041 224159 224363 224580 224662 224941 225023 225194 225220 225245 225389 225498 225590 225725 226178 226829 227036 227242 227609 227844 227880 228064 228365 228618 229052 229189 230055 230117 230248 230257 230283 230438 230750 230977 231001 231086 231157 231413 231617 231722 232355 232384 232427 233103 233637 233713 234069 234306 234571 234639 234950 235043 235086 235408 235656 235720 235747 235811 236038 236217 236555 236663 237255 237348 237368 237596 237670 237998 238015 238163 238312 238623 238804 238815 239099 239218 239293 239345 240021 240725 241071 241153 241159 241466 241474 241668 242119 242151 242383 242913 243159 243198 243697 243819 244187 244456 244886 244957 245322 245582 245833 246119 246562 246747 246812 247035 247152 247327 247479 247523 247534 247545 247910 247962 248062 248353 248430 248788 248949 249169 249174 249635 249719 249837 250262 250436 250450 250463 250518 250539 250696 251259 251921 252185 252190 252199 252254 252298 252529 252543 253323 253583 254021 254353 254835 254928 255218 255548 255881 256422 256841 257020 257355 257382 257423 257600 257955 258105 258129 258957 259440 259496 259566 259603 259743 259779 259950 260163 260188 260301 260344 260533 260646 261855 261983 262160 262190 262380 262417 262645 263753 263918 264539 264642 264897 264910 264999 265084 265103 265145 265254 265718 265736 265739 265826 266019 266454 266599 266957 266980 267352 267373 267610 267773 267807 267871 268463 268483 268771 268913 268931 269203 269438 269731 269926 270390 270497 270738 270847 270981 271043 271136 271221 271266 271737 271782 271998 272001 272382 272453 272507 272523 272772 272980 273042 273432 273472 273561 273597 273939 273982 274018 274321 274479 274635 274808 275041 275103 275125 275430 275618 275782 275905 275919 276032 276165 276254 276601 276625 276844 276895 277087 277191 277341 277716 278184 278322 278331 278423 278626 278724 278829 279034 279123 279136 279507 279542 279818 279825 280314 280689 280816 280986 281207 281323 281327 281658 281978 282224 282814 282862 282917 283237 283298 283336 283446 283722 283883 283950 284229 284485 284625 284731 284829 285055 285124 285545 285594 285723 285746 286043 286362 286439 286449 286532 286653 287082 287261 287474 287486 287541 287568 287629 287966 288182 288344 288463 288543 289066 289258 289299 289593 289624 289693 289727 289792 289913 290106 290118 290216 290347 290385 290655 291146 291358 291604 291768 291929 292359 292401 292584 292752 292857 292943 293175 293204 293222 293757 293814 293972 294264 294597 294678 294684 294849 295712 295830 295883 295909 296170 296228 296321 296514 296583 296901 296965 297110 297211 297855 298185 298984 299447 299541 299593 299669 299818 299821 300195 300225 300399 300403 300641 301143 301460 301534 301840 301847 301942 302025 302139 302281 302615 302776 302859 303006 303615 303768 303770 304057 304090 304368 304407 304508 304543 304672 304723 304957 305034 305233 305345 305446 306196 306383 306484 306600 306793 306860 306890 307078 307107 307242 307641 308026 308211 308258 308451 308541 308655 308928 309744 309924 310053 310137 310217 310548 310942 311190 311234 311771 312000 312242 312604 312696 312697 313115 313435 313554 314346 314358 314382 314495 314588 314840 314894 315049 315116 315129 315240 315311 315361 315779 316289 316316 316492 317020 317079 317211 317437 318343 318436 318621 318657 318682 319663 319723 319909 320120 320237 320331 320604 320739 320887 320981 321049 321097 321331 321466 321728 321798 322249 322308 322402 322505 322507 322560 322729 322744 322973 322982 323052 323057 323115 323192 323452 323481 323693 323905 324056 324776 324948 325070 325101 325198 325241 325624 326021 326062 327019 328014 328048 329289 329513 330159 330315 330320 330843 331295 331449 331578 332232 332391 332406 332563 332742 333306 333703 333874 333891 334002 334027 334124 334376 334522 334932 335390 335572 335703 335903 336181 336250 336390 336608 336835 337265 337448 337532 337595 337815 338103 338279 338375 338604 338613 338915 339202 339413 339965 340070 340175 340229 340279 340455 340622 340722 340959 341255 341745 341756 341764 342150 342233 342573 342726 342833 343067 343129 343303 343574 343655 343716 343757 343912 344296 344372 344475 344546 344729 345333 345990 346407 346558 346652 346743 346745 347001 347066 347557 347604 347833 348772 348838 349152 349418 349617 350596 350727 350778 350915 351000 351007 351038 351520 352036 352309 352461 352535 352975 353035 353258 353550 353577 354064 354274 354885 355017 355330 355347 355694 355787 355968 356005 357042 357107 357373 357388 357487 357526 357550 357603 357658 357891 358018 358042 358204 358571 358856 359399 359525 359682 359980 360668 360836 360856 360988 361431 361634 361809 362366 362530 362610 362725 363205 363605 363810 363930 363982 364597 364618 364860 364885 364900 364907 364942 365011 365066 365146 365437 365455 365506 365712 365817 365916 365950 366082 366109 366172 366661 366776 366901 366946 368106 368138 368500 368725 368833 369405 369494 369686 370187 370232 370476 370673 370690 370802 371104 371372 371400 371482 371813 371822 371934 371999 372013 372054 372063 372183 372355 372689 372842 372967 373184 373760 374148 374446 374529 375088 375227 375365 375414 376181 376196 376224 376321 376374 376541 377153 377477 377702 377809 377820 377952 378136 378627 378732 378907 379074 379319 379465 379644 379698 379822 379970 380055 380680 380845 380877 380939 380989 381212 381441 381632 381641 381836 381952 382076 382193 382203 382238 382401 382548 382653 382981 383404 383436 383468 383471 383768 383901 383903 384155 384839 385227 385513 385756 385829 385905 386161 386175 386388 386672 386856 386973 386997 387048 387084 387193 387797 387800 387886 388062 388430 388454 388559 388613 388700 388767 388816 388879 388915 389098 389455 389801 390269 391186 391246 391405 391414 391834 391996 392473 392814 392856 392943 392946 393231 393317 393348 393699 393765 393966 394003 394137 394151 394204 394245 394277 394682 394890 394925 394985 395502 395915 396027 396100 396184 396221 396571 396651 396715 397468 398328 398353 398461 398497 398613 398844 399406 399664 399747 399851 399853 400365 400396 400751 401596 401832 401909 402145 402690 402753 402787 402873 403028 403624 403808 403986 404037 404260 404475 404653 404712 404724 405024 405286 405624 405880 406022 406091 406226 406227 406510 406629 406741 406782 406864 406969 407156 407452 407591 407818 407980 408098 408198 408528 408760 409049 409088 409335 409354 409834 409860 409947 410006 410043 410193 410348 410373 410693 410723 410837 410920 410923 411251 411270 411378 411411 411560 411961 412047 412154 412194 412257 412336 412736 412816 412940 413027 413157 413560 413577 414175 414273 414425 414492 415437 415658 415698 416058 416592 416768 416893 417046 417212 417320 417470 417959 418014 418398 418602 418838 418929 418998 419070 419192 419250 419571 420062 420097 420098 420134 420163 420194 420404 420486 420680 420959 421082 421537 422078 422521 422561 422576 422672 422747 423034 423279 423385 423415 423506 423534 423704 424067 424094 424180 424617 424670 424833 424932 425084 425221 425360 425380 425407 425498 425604 426989 427263 427613 427626 428002 428245 428539 428666 428706 428747 428963 429449 429487 429584 429662 429676 429871 429950 430605 430792 431172 431309 431455 431924 432297 432435 433314 433410 433415 433488 433552 433588 433729 433888 433896 434005 434074 434131 434212 434261 434301 434521 434548 434673 435076 435245 436080 436147 436400 436460 436573 436972 437359 437575 437577 437623 437668 437765 437782 437815 437849 438174 438248 438368 439189 439199 439399 439554 439593 439622 439995 440181 440256 440299 440347 440509 440622 440939 440966 441335 441352 441360 441487 441596 442082 442470 442537 443551 443962 443997 444050 444135 444269 444282 444302 444574 444629 444653 444726 444758 444964 445061 445294 445357 445573 445694 445790 446125 446269 446364 446491 446593 447097 447247 447891 447892 447913 447993 448280 448388 448423 448457 448784 448949 449020 449194 449212 449284 449674 449877 449923 450580 450686 450765 450828 451136 451162 451508 451602 452066 452464 453042 453100 453174 453199 453303 453454 453642 453871 454168 454219 454241 454896 454924 454964 454976 455195 455260 455537 455681 455871 455972 456227 456261 456344 456418 457030 457392 457680 457764 458152 458190 458321 458482 458652 458803 459129 459136 459177 459622 459661 459935 459984 460033 460375 460534 460703 460782 460843 461255 461402 461453 461475 461538 461658 462098 462734 462787 462808 462854 462867 463166 463353 463425 463480 463536 463590 463880 464094 464347 464424 464546 464701 465110 465129 465294 465321 465903 466000 466107 466243 466402 466406 466554 466632 466635 467083 467436 467705 468401 468570 468900 468918 469033 469268 469668 469699 469758 470469 470740 470769 470841 471123 471346 471487 471500 471512 471714 472100 472629 472653 472896 473080 473088 473386 473731 473786 473898 474000 474014 474217 474361 474567 474900 475168 475587 475841 475920 476196 476224 476532 476568 476683 476882 477082 477219 477410 477764 478066 478158 478375 478445 478555 478833 478975 479419 479630 479824 479980 480105 480154 480180 480416 480578 480680 481125 481782 481811 481918 482049 482101 482222 482252 482328 482990 483201 483347 483672 484073 484293 484414 484783 485136 485595 485757 485843 486052 486268 486308 486392 486487 486648 486747 486748 486865 487446 487531 487555 488061 488541 488604 489240 489864 490324 490763 491028 491158 491392 491660 491788 492142 492145 492166 492412 492926 492951 493517 493583 493754 493859 494021 494046 494097 494198 494379 494528 494685 494894 495280 495548 495571 495653 495947 496268 496513 496667 496720 496849 497045 497297 497668 497760 497794 497959 498089 498519 498632 498671 498775 498776 498791 498919 499038 499190 499849 499985 500258 500608 501592 501608 501665 502124 502400 502570 502660 502957 503052 503948 504005 504064 504509 504746 504936 504956 505163 505247 505260 505278 505538 505618 506045 506650 506679 506751 506970 507190 507695 507731 507734 507802 507940 508067 508290 508361 508405 508480 508634 509028 509239 509377 509690 509789 509938 510092 510468 510475 510536 510552 511151 511174 511205 511213 511409 511484 511864 511962 511963 512202 512514 512705 512837 512901 512930 512936 513088 513451 513624 513936 514014 514074 514774 514852 514985 515287 515311 515714 516004 516051 516151 516353 516497 516530 516631 516893 516917 516977 517151 517316 517805 518465 518679 519159 519229 520201 520403 520493 520551 520784 521024 521163 521605 521845 522059 522063 522309 522569 522999 523389 523438 523559 523736 523754 523981 524018 524277 524633 524651 524837 524870 524940 524957 524982 525127 525328 525740 525760 525768 526144 526181 526620 526953 527295 527411 527785 527787 527939 528217 528374 528421 529216 529374 529379 529646 529896 530014 530518 530688 530878 530901 530974 530991 531191 531508 531735 531880 532170 532176 532241 532285 532481 532653 532758 533040 533134 533211 533522 533656 533953 534052 534487 534857 534952 535421 535516 535576 535621 536086 536165 536255 536417 536492 536989 537108 537109 537174 537982 538424 538639 538887 539269 539432 539516 539577 539700 539726 539776 540469 540636 540781 541052 541383 541421 541464 541523 541592 542210 542637 543169 543187 543565 543610 543877 544095 544219 544454 544464 544533 544910 545030 545429 545675 545992 546017 546235 546479 546497 547078 547200 547211 547439 547473 547824 547989 548019 548039 548309 548319 548431 548720 548981 549425 549460 549466 549557 550060 550096 550380 550543 550664 551199 551208 551388 551391 551414 551508 551595 552896 553188 553437 553515 553741 553864 553913 554112 554162 554220 554294 554327 554446 554576 554807 554973 555034 555092 555140 555192 555228 555394 555561 555784 555789 555825 555909 556087 556109 556176 556198 556525 556714 557062 557181 557753 557765 558301 558496 558613 558673 558900 558910 559062 559085 559485 559702 559962 560041 560286 560342 560365 560859 560871 561184 561210 561234 561298 561308 561561 561671 561737 561778 562132 562247 562473 562785 562795 563092 563281 563469 563662 564082 564122 564203 564426 564434 564585 564604 564629 564775 565027 565351 565531 565617 565944 566082 566144 566366 566530 566916 567030 567258 567820 567913 567922 567923 568012 568102 568298 568427 568599 568798 568816 568890 569051 569088 569225 569245 569873 569876 570008 570204 570205 570227 570660 570868 571041 571352 571361 571564 571581 572061 572652 572782 572929 573118 573506 574112 574584 575374 575400 575468 575594 575706 576033 576113 576402 576525 576572 576793 576979 577074 577094 577331 577529 577536 577565 577605 577783 578040 578139 578699 578703 578810 578853 578910 579373 579439 579524 580120 580163 580387 580776 580825 580920 581322 581855 582861 583312 583470 583990 584154 584334 584469 584527 584554 584566 584810 584829 585459 585460 585572 585598 585912 585980 585992 586046 586284 586340 586687 586727 586739 587002 587185 587836 587977 587980 588037 588294 588536 588755 588896 588900 588918 589187 589292 589372 589486 589512 589993 590239 590300 590306 590661 590897 590913 591000 591079 591100 591123 591449 591482 591503 591719 591887 591906 592298 592307 592476 592544 592863 592885 592944 592961 593076 593237 593482 593962 594049 594177 594189 594610 595333 595531 595593 595627 595770 595834 Warning: split frame 596220 is out of bounds; ignoring. Writing 'ctraj.c0' as Amber NetCDF Writing 'ctraj.c1' as Amber NetCDF Writing 'ctraj.c2' as Amber NetCDF Writing 'ctraj.c3' as Amber NetCDF Writing 'ctraj.c4' as Amber NetCDF Writing 'ctraj.c5' as Amber NetCDF Writing 'rep.c0.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c1.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c2.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c3.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c4.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c5.pdb' as PDB Warning: No PDB space group specified. Cluster timing data: TIME: Cluster Init. : 0.0004 s (0.00%) TIME: Pairwise Calc.: 6.2214 s (1.31%) TIME: Clustering : 1.3461 s (0.28%) TIME: Cluster Post. : 465.9393 s (98.40%) TIME: Total: 473.5073 s TIME: Analyses took 473.5077 seconds. DATASETS: 3 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 596220 _DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 596220 (470.80 MB) Box Coords, 67 atoms Cnum_00002 "Cnum_00002" (integer), size is 596220 DATAFILES: test.dat (Standard Data File): RMSD_00000 ---------- RUN END --------------------------------------------------- TIME: Total execution time: 7486.9985 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.