
  \-/  
  -/-   PTRAJ: a utility for processing trajectory files
  /-\  
  \-/   Version: "AMBER 10.0 integrated" (2/15/2008)
  -/-   Executable is: "ptraj"
  /-\  
  \-/   Residue labels:

 ALA  ALA  LYS  ASP  VAL  LYS  PHE  GLY  ASN  ASP 
 ALA  ARG  VAL  LYS  MET  LEU  ARG  GLY  VAL  ASN 
 VAL  LEU  ALA  ASP  ALA  VAL  LYS  VAL  THR  LEU 
 GLY  PRO  LYS  GLY  ARG  ASN  VAL  VAL  LEU  ASP 
 LYS  SER  PHE  GLY  ALA  PRO  THR  ILE  THR  LYS 
 ASP  GLY  VAL  SER  VAL  ALA  ARG  GLU  ILE  GLU 
 LEU  GLU  ASP  LYS  PHE  GLU  ASN  MET  GLY  ALA 
 GLN  MET  VAL  LYS  GLU  VAL  ALA  SER  LYS  ALA 
 ASN  ASP  ALA  ALA  GLY  ASP  GLY  THR  THR  THR 
 ALA  THR  VAL  LEU  ALA  GLN  ALA  ILE  ILE  THR 
 GLU  GLY  LEU  LYS  ALA  VAL  ALA  ALA  GLY  MET 
 ASN  PRO  MET  ASP  LEU  LYS  ARG  GLY  ILE  ASP 
 LYS  ALA  VAL  THR  ALA  ALA  VAL  GLU  GLU  LEU 
 LYS  ALA  LEU  SER  VAL  PRO  CYS  SER  ASP  SER 
 LYS  ALA  ILE  ALA  GLN  VAL  GLY  THR  ILE  SER 
 ALA  ASN  SER  ASP  GLU  THR  VAL  GLY  LYS  LEU 
 ILE  ALA  GLU  ALA  MET  ASP  LYS  VAL  GLY  LYS 
 GLU  GLY  VAL  ILE  THR  VAL  GLU  ASP  GLY  THR 
 GLY  LEU  GLN  ASP  GLU  LEU  ASP  VAL  VAL  GLU 
 GLY  MET  GLN  PHE  ASP  ARG  GLY  TYR  LEU  SER 
 PRO  TYR  PHE  ILE  ASN  LYS  PRO  GLU  THR  GLY 
 ALA  VAL  GLU  LEU  GLU  SER  PRO  PHE  ILE  LEU 
 LEU  ALA  ASP  LYS  LYS  ILE  SER  ASN  ILE  ARG 
 GLU  MET  LEU  PRO  VAL  LEU  GLU  ALA  VAL  ALA 
 LYS  ALA  GLY  LYS  PRO  LEU  LEU  ILE  ILE  ALA 
 GLU  ASP  VAL  GLU  GLY  GLU  ALA  LEU  ALA  THR 
 LEU  VAL  VAL  ASN  THR  MET  ARG  GLY  ILE  VAL 
 LYS  VAL  ALA  ALA  VAL  LYS  ALA  PRO  GLY  PHE 
 GLY  ASP  ARG  ARG  LYS  ALA  MET  LEU  GLN  ASP 
 ILE  ALA  THR  LEU  THR  GLY  GLY  THR  VAL  ILE 
 SER  GLU  GLU  ILE  GLY  MET  GLU  LEU  GLU  LYS 
 ALA  THR  LEU  GLU  ASP  LEU  GLY  GLN  ALA  LYS 
 ARG  VAL  VAL  ILE  ASN  LYS  ASP  THR  THR  THR 
 ILE  ILE  ASP  GLY  VAL  GLY  GLU  GLU  ALA  ALA 
 ILE  GLN  GLY  ARG  VAL  ALA  GLN  ILE  ARG  GLN 
 GLN  ILE  GLU  GLU  ALA  THR  SER  ASP  TYR  ASP 
 ARG  GLU  LYS  LEU  GLN  GLU  ARG  VAL  ALA  LYS 
 LEU  ALA  GLY  GLY  VAL  ALA  VAL  ILE  LYS  VAL 
 GLY  ALA  ALA  THR  GLU  VAL  GLU  MET  LYS  GLU 
 LYS  LYS  ALA  ARG  VAL  GLU  ASP  ALA  LEU  HID 
 ALA  THR  ARG  ALA  ALA  VAL  GLU  GLU  GLY  VAL 
 VAL  ALA  GLY  GLY  GLY  VAL  ALA  LEU  ILE  ARG 
 VAL  ALA  SER  LYS  LEU  ALA  ASP  LEU  ARG  GLY 
 GLN  ASN  GLU  ASP  GLN  ASN  VAL  GLY  ILE  LYS 
 VAL  ALA  LEU  ARG  ALA  MET  GLU  ALA  PRO  LEU 
 ARG  GLN  ILE  VAL  LEU  ASN  CYS  GLY  GLU  GLU 
 PRO  SER  VAL  VAL  ALA  ASN  THR  VAL  LYS  GLY 
 GLY  ASP  GLY  ASN  TYR  GLY  TYR  ASN  ALA  ALA 
 THR  GLU  GLU  TYR  GLY  ASN  MET  ILE  ASP  MET 
 GLY  ILE  LEU  ASP  PRO  THR  LYS  VAL  THR  ARG 
 SER  ALA  LEU  GLN  TYR  ALA  ALA  SER  VAL  ALA 
 GLY  LEU  MET  ILE  THR  THR  GLU  CYS  MET  VAL 
 THR  ASP  LEU  PRO  WAT  WAT  WAT  WAT  WAT  WAT 
 WAT  WAT  WAT  WAT  WAT  WAT  WAT  WAT  WAT  WAT 
 ...

 Setting box to be an exact truncated octahedron, angle is 109.471221

PTRAJ: Processing input from file rmsd.ptraj

PTRAJ: trajin ../traj/1-50ns_imposedOnStart.nc
  Checking coordinates: ../traj/1-50ns_imposedOnStart.nc

PTRAJ: trajin ../traj/51-100ns_imposedOnStart.nc
  Checking coordinates: ../traj/51-100ns_imposedOnStart.nc

PTRAJ: trajin ../traj/101-150ns_imposedOnStart.nc
  Checking coordinates: ../traj/101-150ns_imposedOnStart.nc

PTRAJ: trajin ../traj/151-200ns_imposedOnStart.nc
  Checking coordinates: ../traj/151-200ns_imposedOnStart.nc

PTRAJ: trajin ../traj/201-250ns_imposedOnStart.nc
  Checking coordinates: ../traj/201-250ns_imposedOnStart.nc

PTRAJ: trajin ../traj/251-300ns_imposedOnStart.nc
  Checking coordinates: ../traj/251-300ns_imposedOnStart.nc

PTRAJ: rms first mass out rmsd.dat @N,CA,C time 0.01
Mask [@N,CA,C] represents 1572 atoms

PTRAJ: rms first mass out rmsd_apical.dat :192-374@N,CA,C time 0.01
Mask [:192-374@N,CA,C] represents 549 atoms

PTRAJ: rms first mass out rmsd_equatorial.dat :1-136,410-524@N,CA,C time 0.01
Mask [:1-136,410-524@N,CA,C] represents 753 atoms

PTRAJ: rms first mass out rmsd_intermediate.dat :137-191,375-409@N,CA,C time 0.01
Mask [:137-191,375-409@N,CA,C] represents 270 atoms
[No output trajectory specified (trajout)]

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 30000 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (../traj/1-50ns_imposedOnStart.nc) is a NetCDF AMBER trajectory with box info with 5000 sets
  File (../traj/51-100ns_imposedOnStart.nc) is a NetCDF AMBER trajectory with box info with 5000 sets
  File (../traj/101-150ns_imposedOnStart.nc) is a NetCDF AMBER trajectory with box info with 5000 sets
  File (../traj/151-200ns_imposedOnStart.nc) is a NetCDF AMBER trajectory with box info with 5000 sets
  File (../traj/201-250ns_imposedOnStart.nc) is a NetCDF AMBER trajectory with box info with 5000 sets
  File (../traj/251-300ns_imposedOnStart.nc) is a NetCDF AMBER trajectory with box info with 5000 sets

NO OUTPUT COORDINATE FILE WAS SPECIFIED

ACTIONS
  1>  RMS to first frame using mass weighting
      Dumping RMSd vs. time (with time interval 0.01) to a file named rmsd.dat
      Atom selection follows :1-524@N,CA,C
  2>  RMS to first frame using mass weighting
      Dumping RMSd vs. time (with time interval 0.01) to a file named rmsd_apical.dat
      Atom selection follows :192-374@N,CA,C
  3>  RMS to first frame using mass weighting
      Dumping RMSd vs. time (with time interval 0.01) to a file named rmsd_equatorial.dat
      Atom selection follows :1-136@N,CA,C,:410-524@N,CA,C
  4>  RMS to first frame using mass weighting
      Dumping RMSd vs. time (with time interval 0.01) to a file named rmsd_intermediate.dat
      Atom selection follows :137-191@N,CA,C,:375-409@N,CA,C


Set      1 .................................................
Set     50 .................................................
Set    100 .................................................
Set    150 .................................................
Set    200 .................................................
Set    250 .................................................
Set    300 .................................................
Set    350 .................................................
Set    400 .................................................
Set    450 .................................................
Set    500 .................................................
Set    550 .................................................
Set    600 .................................................
Set    650 .................................................
Set    700 .................................................
Set    750 .................................................
Set    800 .................................................
Set    850 .................................................
Set    900 .................................................
Set    950 .................................................
Set   1000 .................................................
Set   1050 .................................................
Set   1100 .................................................
Set   1150 .................................................
Set   1200 .................................................
Set   1250 .................................................
Set   1300 .................................................
Set   1350 .................................................
Set   1400 .................................................
Set   1450 .................................................
Set   1500 .................................................
Set   1550 .................................................
Set   1600 .................................................
Set   1650 .................................................
Set   1700 .................................................
Set   1750 .................................................
Set   1800 .................................................
Set   1850 .................................................
Set   1900 .................................................
Set   1950 .................................................
Set   2000 .................................................
Set   2050 .................................................
Set   2100 .................................................
Set   2150 .................................................
Set   2200 .................................................
Set   2250 .................................................
Set   2300 .................................................
Set   2350 .................................................
Set   2400 .................................................
Set   2450 .................................................
Set   2500 .................................................
Set   2550 .................................................
Set   2600 .................................................
Set   2650 .................................................
Set   2700 .................................................
Set   2750 .................................................
Set   2800 .................................................
Set   2850 .................................................
Set   2900 .................................................
Set   2950 .................................................
Set   3000 .................................................
Set   3050 .................................................
Set   3100 .................................................
Set   3150 .................................................
Set   3200 .................................................
Set   3250 .................................................
Set   3300 .................................................
Set   3350 .................................................
Set   3400 .................................................
Set   3450 .................................................
Set   3500 .................................................
Set   3550 .................................................
Set   3600 .................................................
Set   3650 .................................................
Set   3700 .................................................
Set   3750 .................................................
Set   3800 .................................................
Set   3850 .................................................
Set   3900 .................................................
Set   3950 .................................................
Set   4000 .................................................
Set   4050 .................................................
Set   4100 .................................................
Set   4150 .................................................
Set   4200 .................................................
Set   4250 .................................................
Set   4300 .................................................
Set   4350 .................................................
Set   4400 .................................................
Set   4450 .................................................
Set   4500 .................................................
Set   4550 .................................................
Set   4600 .................................................
Set   4650 .................................................
Set   4700 .................................................
Set   4750 .................................................
Set   4800 .................................................
Set   4850 .................................................
Set   4900 .................................................
Set   4950 .................................................
Set   5000 
Set      1 .................................................
Set     50 .................................................
Set    100 .................................................
Set    150 .................................................
Set    200 .................................................
Set    250 .................................................
Set    300 .................................................
Set    350 .................................................
Set    400 .................................................
Set    450 .................................................
Set    500 .................................................
Set    550 .................................................
Set    600 .................................................
Set    650 .................................................
Set    700 .................................................
Set    750 .................................................
Set    800 .................................................
Set    850 .................................................
Set    900 .................................................
Set    950 .................................................
Set   1000 .................................................
Set   1050 .................................................
Set   1100 .................................................
Set   1150 .................................................
Set   1200 .................................................
Set   1250 .................................................
Set   1300 .................................................
Set   1350 .................................................
Set   1400 .................................................
Set   1450 .................................................
Set   1500 .................................................
Set   1550 .................................................
Set   1600 .................................................
Set   1650 .................................................
Set   1700 .................................................
Set   1750 .................................................
Set   1800 .................................................
Set   1850 .................................................
Set   1900 .................................................
Set   1950 .................................................
Set   2000 .................................................
Set   2050 .................................................
Set   2100 .................................................
Set   2150 .................................................
Set   2200 .................................................
Set   2250 .................................................
Set   2300 .................................................
Set   2350 .................................................
Set   2400 .................................................
Set   2450 .................................................
Set   2500 .................................................
Set   2550 .................................................
Set   2600 .................................................
Set   2650 .................................................
Set   2700 .................................................
Set   2750 .................................................
Set   2800 .................................................
Set   2850 .................................................
Set   2900 .................................................
Set   2950 .................................................
Set   3000 .................................................
Set   3050 .................................................
Set   3100 .................................................
Set   3150 .................................................
Set   3200 .................................................
Set   3250 .................................................
Set   3300 .................................................
Set   3350 .................................................
Set   3400 .................................................
Set   3450 .................................................
Set   3500 .................................................
Set   3550 .................................................
Set   3600 .................................................
Set   3650 .................................................
Set   3700 .................................................
Set   3750 .................................................
Set   3800 .................................................
Set   3850 .................................................
Set   3900 .................................................
Set   3950 .................................................
Set   4000 .................................................
Set   4050 .................................................
Set   4100 .................................................
Set   4150 .................................................
Set   4200 .................................................
Set   4250 .................................................
Set   4300 .................................................
Set   4350 .................................................
Set   4400 .................................................
Set   4450 .................................................
Set   4500 .................................................
Set   4550 .................................................
Set   4600 .................................................
Set   4650 .................................................
Set   4700 .................................................
Set   4750 .................................................
Set   4800 .................................................
Set   4850 .................................................
Set   4900 .................................................
Set   4950 .................................................
Set   5000 
Set      1 .................................................
Set     50 .................................................
Set    100 .................................................
Set    150 .................................................
Set    200 .................................................
Set    250 .................................................
Set    300 .................................................
Set    350 .................................................
Set    400 .................................................
Set    450 .................................................
Set    500 .................................................
Set    550 .................................................
Set    600 .................................................
Set    650 .................................................
Set    700 .................................................
Set    750 .................................................
Set    800 .................................................
Set    850 .................................................
Set    900 .................................................
Set    950 .................................................
Set   1000 .................................................
Set   1050 .................................................
Set   1100 .................................................
Set   1150 .................................................
Set   1200 .................................................
Set   1250 .................................................
Set   1300 .................................................
Set   1350 .................................................
Set   1400 .................................................
Set   1450 .................................................
Set   1500 .................................................
Set   1550 .................................................
Set   1600 .................................................
Set   1650 .................................................
Set   1700 .................................................
Set   1750 .................................................
Set   1800 .................................................
Set   1850 .................................................
Set   1900 .................................................
Set   1950 .................................................
Set   2000 .................................................
Set   2050 .................................................
Set   2100 .................................................
Set   2150 .................................................
Set   2200 .................................................
Set   2250 .................................................
Set   2300 .................................................
Set   2350 .................................................
Set   2400 .................................................
Set   2450 .................................................
Set   2500 .................................................
Set   2550 .................................................
Set   2600 .................................................
Set   2650 .................................................
Set   2700 .................................................
Set   2750 .................................................
Set   2800 .................................................
Set   2850 .................................................
Set   2900 .................................................
Set   2950 .................................................
Set   3000 .................................................
Set   3050 .................................................
Set   3100 .................................................
Set   3150 .................................................
Set   3200 .................................................
Set   3250 .................................................
Set   3300 .................................................
Set   3350 .................................................
Set   3400 .................................................
Set   3450 .................................................
Set   3500 .................................................
Set   3550 .................................................
Set   3600 .................................................
Set   3650 .................................................
Set   3700 .................................................
Set   3750 .................................................
Set   3800 .................................................
Set   3850 .................................................
Set   3900 .................................................
Set   3950 .................................................
Set   4000 .................................................
Set   4050 .................................................
Set   4100 .................................................
Set   4150 .................................................
Set   4200 .................................................
Set   4250 .................................................
Set   4300 .................................................
Set   4350 .................................................
Set   4400 .................................................
Set   4450 .................................................
Set   4500 .................................................
Set   4550 .................................................
Set   4600 .................................................
Set   4650 .................................................
Set   4700 .................................................
Set   4750 .................................................
Set   4800 .................................................
Set   4850 .................................................
Set   4900 .................................................
Set   4950 .................................................
Set   5000 
Set      1 .................................................
Set     50 .................................................
Set    100 .................................................
Set    150 .................................................
Set    200 .................................................
Set    250 .................................................
Set    300 .................................................
Set    350 .................................................
Set    400 .................................................
Set    450 .................................................
Set    500 .................................................
Set    550 .................................................
Set    600 .................................................
Set    650 .................................................
Set    700 .................................................
Set    750 .................................................
Set    800 .................................................
Set    850 .................................................
Set    900 .................................................
Set    950 .................................................
Set   1000 .................................................
Set   1050 .................................................
Set   1100 .................................................
Set   1150 .................................................
Set   1200 .................................................
Set   1250 .................................................
Set   1300 .................................................
Set   1350 .................................................
Set   1400 .................................................
Set   1450 .................................................
Set   1500 .................................................
Set   1550 .................................................
Set   1600 .................................................
Set   1650 .................................................
Set   1700 .................................................
Set   1750 .................................................
Set   1800 .................................................
Set   1850 .................................................
Set   1900 .................................................
Set   1950 .................................................
Set   2000 .................................................
Set   2050 .................................................
Set   2100 .................................................
Set   2150 .................................................
Set   2200 .................................................
Set   2250 .................................................
Set   2300 .................................................
Set   2350 .................................................
Set   2400 .................................................
Set   2450 .................................................
Set   2500 .................................................
Set   2550 .................................................
Set   2600 .................................................
Set   2650 .................................................
Set   2700 .................................................
Set   2750 .................................................
Set   2800 .................................................
Set   2850 .................................................
Set   2900 .................................................
Set   2950 .................................................
Set   3000 .................................................
Set   3050 .................................................
Set   3100 .................................................
Set   3150 .................................................
Set   3200 .................................................
Set   3250 .................................................
Set   3300 .................................................
Set   3350 .................................................
Set   3400 .................................................
Set   3450 .................................................
Set   3500 .................................................
Set   3550 .................................................
Set   3600 .................................................
Set   3650 .................................................
Set   3700 .................................................
Set   3750 .................................................
Set   3800 .................................................
Set   3850 .................................................
Set   3900 .................................................
Set   3950 .................................................
Set   4000 .................................................
Set   4050 .................................................
Set   4100 .................................................
Set   4150 .................................................
Set   4200 .................................................
Set   4250 .................................................
Set   4300 .................................................
Set   4350 .................................................
Set   4400 .................................................
Set   4450 .................................................
Set   4500 .................................................
Set   4550 .................................................
Set   4600 .................................................
Set   4650 .................................................
Set   4700 .................................................
Set   4750 .................................................
Set   4800 .................................................
Set   4850 .................................................
Set   4900 .................................................
Set   4950 .................................................
Set   5000 
Set      1 .................................................
Set     50 .................................................
Set    100 .................................................
Set    150 .................................................
Set    200 .................................................
Set    250 .................................................
Set    300 .................................................
Set    350 .................................................
Set    400 .................................................
Set    450 .................................................
Set    500 .................................................
Set    550 .................................................
Set    600 .................................................
Set    650 .................................................
Set    700 .................................................
Set    750 .................................................
Set    800 .................................................
Set    850 .................................................
Set    900 .................................................
Set    950 .................................................
Set   1000 .................................................
Set   1050 .................................................
Set   1100 .................................................
Set   1150 .................................................
Set   1200 .................................................
Set   1250 .................................................
Set   1300 .................................................
Set   1350 .................................................
Set   1400 .................................................
Set   1450 .................................................
Set   1500 .................................................
Set   1550 .................................................
Set   1600 .................................................
Set   1650 .................................................
Set   1700 .................................................
Set   1750 .................................................
Set   1800 .................................................
Set   1850 .................................................
Set   1900 .................................................
Set   1950 .................................................
Set   2000 .................................................
Set   2050 .................................................
Set   2100 .................................................
Set   2150 .................................................
Set   2200 .................................................
Set   2250 .................................................
Set   2300 .................................................
Set   2350 .................................................
Set   2400 .................................................
Set   2450 .................................................
Set   2500 .................................................
Set   2550 .................................................
Set   2600 .................................................
Set   2650 .................................................
Set   2700 .................................................
Set   2750 .................................................
Set   2800 .................................................
Set   2850 .................................................
Set   2900 .................................................
Set   2950 .................................................
Set   3000 .................................................
Set   3050 .................................................
Set   3100 .................................................
Set   3150 .................................................
Set   3200 .................................................
Set   3250 .................................................
Set   3300 .................................................
Set   3350 .................................................
Set   3400 .................................................
Set   3450 .................................................
Set   3500 .................................................
Set   3550 .................................................
Set   3600 .................................................
Set   3650 .................................................
Set   3700 .................................................
Set   3750 .................................................
Set   3800 .................................................
Set   3850 .................................................
Set   3900 .................................................
Set   3950 .................................................
Set   4000 .................................................
Set   4050 .................................................
Set   4100 .................................................
Set   4150 .................................................
Set   4200 .................................................
Set   4250 .................................................
Set   4300 .................................................
Set   4350 .................................................
Set   4400 .................................................
Set   4450 .................................................
Set   4500 .................................................
Set   4550 .................................................
Set   4600 .................................................
Set   4650 .................................................
Set   4700 .................................................
Set   4750 .................................................
Set   4800 .................................................
Set   4850 .................................................
Set   4900 .................................................
Set   4950 .................................................
Set   5000 
Set      1 .................................................
Set     50 .................................................
Set    100 .................................................
Set    150 .................................................
Set    200 .................................................
Set    250 .................................................
Set    300 .................................................
Set    350 .................................................
Set    400 .................................................
Set    450 .................................................
Set    500 .................................................
Set    550 .................................................
Set    600 .................................................
Set    650 .................................................
Set    700 .................................................
Set    750 .................................................
Set    800 .................................................
Set    850 .................................................
Set    900 .................................................
Set    950 .................................................
Set   1000 .................................................
Set   1050 .................................................
Set   1100 .................................................
Set   1150 .................................................
Set   1200 .................................................
Set   1250 .................................................
Set   1300 .................................................
Set   1350 .................................................
Set   1400 .................................................
Set   1450 .................................................
Set   1500 .................................................
Set   1550 .................................................
Set   1600 .................................................
Set   1650 .................................................
Set   1700 .................................................
Set   1750 .................................................
Set   1800 .................................................
Set   1850 .................................................
Set   1900 .................................................
Set   1950 .................................................
Set   2000 .................................................
Set   2050 .................................................
Set   2100 .................................................
Set   2150 .................................................
Set   2200 .................................................
Set   2250 .................................................
Set   2300 .................................................
Set   2350 .................................................
Set   2400 .................................................
Set   2450 .................................................
Set   2500 .................................................
Set   2550 .................................................
Set   2600 .................................................
Set   2650 .................................................
Set   2700 .................................................
Set   2750 .................................................
Set   2800 .................................................
Set   2850 .................................................
Set   2900 .................................................
Set   2950 .................................................
Set   3000 .................................................
Set   3050 .................................................
Set   3100 .................................................
Set   3150 .................................................
Set   3200 .................................................
Set   3250 .................................................
Set   3300 .................................................
Set   3350 .................................................
Set   3400 .................................................
Set   3450 .................................................
Set   3500 .................................................
Set   3550 .................................................
Set   3600 .................................................
Set   3650 .................................................
Set   3700 .................................................
Set   3750 .................................................
Set   3800 .................................................
Set   3850 .................................................
Set   3900 .................................................
Set   3950 .................................................
Set   4000 .................................................
Set   4050 .................................................
Set   4100 .................................................
Set   4150 .................................................
Set   4200 .................................................
Set   4250 .................................................
Set   4300 .................................................
Set   4350 .................................................
Set   4400 .................................................
Set   4450 .................................................
Set   4500 .................................................
Set   4550 .................................................
Set   4600 .................................................
Set   4650 .................................................
Set   4700 .................................................
Set   4750 .................................................
Set   4800 .................................................
Set   4850 .................................................
Set   4900 .................................................
Set   4950 .................................................
Set   5000 

PTRAJ: Successfully read in 30000 sets and processed 30000 sets.
       Dumping accumulated results (if any)

PTRAJ RMS: dumping RMSd vs time data
PTRAJ RMS: dumping RMSd vs time data
PTRAJ RMS: dumping RMSd vs time data
PTRAJ RMS: dumping RMSd vs time data
