CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/04/15 14:09:24 | Available memory: 15439.2 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 8 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 8 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 0.0017 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: 7003.7963 s TIME: Avg. throughput= 85.1281 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 8 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 (1178200000) 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: 2974 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 259 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 88 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 37 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 64 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 134 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 180 points changed cluster assignment. Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 7: 160 points changed cluster assignment. Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 8: 66 points changed cluster assignment. Round 9: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 9: 64 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: 19 points changed cluster assignment. Round 12: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 12: 9 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: 4 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: 8 clusters 596220 frames #Cluster 0 has average-distance-to-centroid 0.858463 #Cluster 1 has average-distance-to-centroid 1.242046 #Cluster 2 has average-distance-to-centroid 0.686942 #Cluster 3 has average-distance-to-centroid 1.032710 #Cluster 4 has average-distance-to-centroid 1.186627 #Cluster 5 has average-distance-to-centroid 1.720269 #Cluster 6 has average-distance-to-centroid 1.612041 #Cluster 7 has average-distance-to-centroid 1.960948 #DBI: 1.430920 #pSF: 147563.806932 #Algorithm: Kmeans nclusters 8 maxit 100 #Representative frames: 127488 145261 104073 530481 149222 435098 571592 468931 #Sieve value: 200 (random) #Sieved frames: 101 108 312 338 391 1933 2141 2466 2487 2651 2680 2839 2841 2895 2927 3112 3516 3649 3824 3919 4647 4650 4769 4861 4873 4944 5413 5430 5791 5838 5958 6069 6194 6465 6697 6901 6939 6956 7048 7323 7423 8331 8627 8907 9063 9343 9870 9902 10036 10165 10259 11058 11346 11530 11603 11621 12298 12679 12912 13784 13971 14134 14595 14731 14917 14970 14971 15420 15439 15965 15993 16067 17519 18124 19267 19624 19921 20065 20417 20568 20666 21095 21194 21248 21342 21407 21484 21516 21588 22004 22172 22277 22300 22341 22343 22492 22521 22582 22590 22862 23567 23621 23853 24010 24589 24824 25053 25262 25626 25740 25754 26073 26128 26145 26273 26285 26537 26594 26625 26934 26944 26958 27001 27005 27652 27741 27781 27810 27957 28088 28824 29228 29488 29573 30000 30206 30269 30299 30498 31191 31321 31527 31798 31839 31975 32175 32305 32362 32644 32649 32711 32920 32961 32968 33148 33230 33500 33587 33683 34274 34477 34766 34894 34949 35402 35602 35859 36343 36505 37111 38111 38233 38339 38420 38447 38534 38759 38901 38992 39006 39054 39498 39614 39625 40180 40212 40250 40354 40394 40773 40956 41292 41448 41564 41688 41810 41905 42129 42964 43218 43304 43389 43517 43683 43736 43764 43775 43899 44850 45059 45098 45366 45714 45983 46072 46346 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538365 538549 538889 539088 539091 539370 539422 539432 539599 539687 540046 540064 540069 540114 540646 540854 541007 541038 541507 541536 541588 541670 541727 541840 542076 542105 542180 542375 542425 542611 542620 543946 544536 544566 544598 544728 545092 545467 545640 545822 545856 545963 545982 546195 546391 546550 546719 546793 547200 547337 547715 547744 547900 548012 548158 548420 548550 548578 548583 548812 549444 549708 549946 550084 550098 550284 550618 551077 551390 551432 551507 551617 551694 551807 551847 552159 552249 552258 552439 552483 552588 552672 552830 553059 553354 553520 553568 553790 553915 554033 554157 554873 554877 554894 554986 555444 555868 556270 556380 556528 556916 556992 557135 557250 557259 557284 557396 558275 558283 558591 558771 558899 559019 559083 559290 559346 559979 560033 560195 560273 560375 560415 560503 560657 560790 561314 561363 561513 561531 561736 562113 562363 563050 563371 563454 563668 563810 563943 563979 564174 564358 564841 564856 565242 565261 565331 565407 565516 565535 565670 565721 566181 566553 566635 566844 567147 567237 567447 567540 567577 567654 567834 568163 568603 568716 569161 569598 569613 569783 570171 570239 570336 570419 570559 570563 571538 571555 571558 571565 571592 571637 571666 571876 572077 572163 572170 572301 572633 572811 573197 573362 573988 574286 574466 574638 575283 575346 575522 575603 575888 575981 576137 576325 576565 576623 576812 577055 577106 577333 578076 578182 578216 578582 579257 579282 579809 579832 579843 580359 580410 580791 580885 581008 581021 581162 581416 581586 581905 581982 582031 582079 582156 582232 582245 582343 582369 582648 582675 582720 582768 583370 583834 584114 584210 584234 584735 584788 585464 585556 585638 585948 586060 586274 586464 586562 586876 586892 586924 587964 588123 588187 588399 588653 588878 589121 589144 589147 589253 589487 589721 589727 589761 589944 589963 590284 590346 590659 591245 591318 591369 591532 591745 591901 592001 592649 592852 592959 593364 593424 593669 593928 594291 594689 594710 595299 595311 595716 595859 595861 595998 596014 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 'ctraj.c6' as Amber NetCDF Writing 'ctraj.c7' 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. Writing 'rep.c6.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c7.pdb' as PDB Warning: No PDB space group specified. Cluster timing data: TIME: Cluster Init. : 0.0005 s (0.00%) TIME: Pairwise Calc.: 7.2386 s (1.52%) TIME: Clustering : 1.6336 s (0.34%) TIME: Cluster Post. : 467.5608 s (98.14%) TIME: Total: 476.4334 s TIME: Analyses took 476.4338 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: 7506.7781 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.