C:\Users\dbuschho\Desktop\Programming\chemistry\molsim\NAMD_2.7b2_Win32\nano_files>dir Directory of C:\Users\dbuschho\Desktop\Programming\chemistry\molsim\NAMD_2.7b2_Win32\nano_files 02/15/2010 09:04 PM . 02/15/2010 09:04 PM .. 02/15/2010 06:59 PM 6,148 .DS_Store 02/15/2010 06:59 PM 101,715 cnt.pdb 02/15/2010 06:59 PM 275,063 cnt.psf 02/15/2010 06:59 PM 275,063 cnt_mod.psf 02/15/2010 06:59 PM 47,592,276 eq.dcd 02/15/2010 06:59 PM 2,074 flow.tcl 02/15/2010 06:59 PM 34,494 imdnanotube.pdb 02/15/2010 06:59 PM 77,878 imdnanotube.psf 02/15/2010 06:59 PM 31,684 initial.coor 02/15/2010 06:59 PM 31,684 initial.vel 02/15/2010 06:59 PM 98,019 nanotubes.pdb 02/15/2010 06:59 PM 259,949 nanotubes.psf 02/15/2010 06:59 PM 123,550 par_all22_prot.inp 02/15/2010 06:59 PM 142,721 par_all27_prot_lipid.prm 02/15/2010 06:59 PM 990 par_nanotubes.inp 02/15/2010 06:59 PM 2,540 permeation.tcl 02/15/2010 06:59 PM 15,864,276 sim.dcd 02/15/2010 06:59 PM 15,864,276 sim_mod.dcd 02/15/2010 09:04 PM 3,292 sim_short.conf 19 File(s) 80,787,692 bytes 2 Dir(s) 175,023,742,976 bytes free C:\Users\dbuschho\Desktop\Programming\chemistry\molsim\NAMD_2.7b2_Win32\nano_files>c:\Users\dbuschho\Desktop\Programming\chemistry\molsim\NAMD_2.7b2_Win32\namd2.exe sim_short.conf Charm++: standalone mode (not using charmrun) CmiMemory: fences and atomic operations not available in native assembly [0] isomalloc.c> Disabling isomalloc because mmap() does not work Charm++> cpu topology info is being gathered. Charm++> Running on 1 unique compute nodes (2-way SMP). Info: NAMD 2.7b2 for Win32 Info: Info: Please visit http://www.ks.uiuc.edu/Research/namd/ Info: and send feedback or bug reports to namd@ks.uiuc.edu Info: Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005) Info: in all publications reporting results obtained with NAMD. Info: Info: Based on Charm++/Converse 60103 for multicore-win32 Info: Built Thu Nov 12 22:32:06 CST 2009 by jcphill on honor Info: Running on 1 processors. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.0450001 s Info: 2.79688 MB of memory in use based on GetProcessMemoryInfo Info: Configuration file is sim_short.conf TCL: Suspending until startup complete. Info: SIMULATION PARAMETERS: Info: TIMESTEP 1 Info: NUMBER OF STEPS 0 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 23 0 0 Info: PERIODIC CELL BASIS 2 0 19.919 0 Info: PERIODIC CELL BASIS 3 0 0 30.3962 Info: PERIODIC CELL CENTER 0 0 0 Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT. Info: LOAD BALANCE STRATEGY New Load Balancers -- ASB Info: LDB PERIOD 4000 steps Info: FIRST LDB TIMESTEP 100 Info: LAST LDB TIMESTEP -1 Info: LDB BACKGROUND SCALING 1 Info: HOM BACKGROUND SCALING 1 Info: MAX SELF PARTITIONS 20 Info: MAX PAIR PARTITIONS 8 Info: SELF PARTITION ATOMS 154 Info: SELF2 PARTITION ATOMS 154 Info: PAIR PARTITION ATOMS 318 Info: PAIR2 PARTITION ATOMS 637 Info: MIN ATOMS PER PATCH 100 Info: VELOCITY FILE initial.vel Info: CENTER OF MASS MOVING INITIALLY? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 SCALE FACTOR 1 Info: DCD FILENAME sim_short.dcd Info: DCD FREQUENCY 1000 Info: DCD FIRST STEP 1000 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME sim_short Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME sim_short.restart Info: RESTART FREQUENCY 1000 Info: BINARY RESTART FILES WILL BE USED Info: SWITCHING ACTIVE Info: SWITCHING ON 10 Info: SWITCHING OFF 12 Info: PAIRLIST DISTANCE 14.5 Info: PAIRLIST SHRINK RATE 0.01 Info: PAIRLIST GROW RATE 0.01 Info: PAIRLIST TRIGGER 0.3 Info: PAIRLISTS PER CYCLE 2 Info: PAIRLISTS ENABLED Info: MARGIN 0 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 17 Info: ENERGY OUTPUT STEPS 1000 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 10000 Info: FIXED ATOMS ACTIVE Info: TCL GLOBAL FORCES ACTIVE Info: TCL GLOBAL FORCES SCRIPT INLINED IN CONFIG FILE Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 300 Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS Info: USING VERLET I (r-RESPA) MTS SCHEME. Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS Info: NONBONDED FORCES EVALUATED EVERY 2 STEPS Info: RANDOM NUMBER SEED 1266289969 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB cnt.pdb Info: STRUCTURE FILE cnt.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS par_all27_prot_lipid.prm Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: BINARY COORDINATES initial.coor Info: SUMMARY OF PARAMETERS: Info: 179 BONDS Info: 441 ANGLES Info: 534 DIHEDRAL Info: 49 IMPROPER Info: 0 CROSSTERM Info: 89 VDW Info: 0 VDW_PAIRS Info: TIME FOR READING PSF FILE: 0.072 Info: TIME FOR READING PDB FILE: 0.00600004 Info: Info: Reading from binary file initial.coor Warning: Converting binary file initial.coor Info: **************************** Info: STRUCTURE SUMMARY: Info: 1320 ATOMS Info: 1312 BONDS Info: 1784 ANGLES Info: 2928 DIHEDRALS Info: 0 IMPROPERS Info: 0 CROSSTERMS Info: 0 EXCLUSIONS Info: 576 FIXED ATOMS Info: 2232 DEGREES OF FREEDOM Info: 824 HYDROGEN GROUPS Info: 576 HYDROGEN GROUPS WITH ALL ATOMS FIXED Info: TOTAL MASS = 11386.2 amu Info: TOTAL CHARGE = 0 e Info: MASS DENSITY = 1.35776 g/cm^3 Info: ATOM DENSITY = 0.0947893 atoms/A^3 Info: ***************************** Info: Info: Entering startup at 0.248 s, 3.67578 MB of memory in use Info: Startup phase 0 took 0.00100017 s, 3.67578 MB of memory in use Info: Startup phase 1 took 0.00399995 s, 4.01953 MB of memory in use Info: Startup phase 2 took 0.000999928 s, 4.01953 MB of memory in use Info: PATCH GRID IS 1 (PERIODIC) BY 1 (PERIODIC) BY 1 (PERIODIC) Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY Info: Reading from binary file initial.vel Warning: Converting binary file initial.vel Info: REMOVING COM VELOCITY 0.11136 -0.035303 0.0929501 Info: LARGEST PATCH (0) HAS 1320 ATOMS Info: CREATING 135 COMPUTE OBJECTS Info: Startup phase 3 took 0.00699997 s, 4.33594 MB of memory in use Info: Startup phase 4 took 0.00100017 s, 4.33594 MB of memory in use Info: Startup phase 5 took 0.000999928 s, 4.33594 MB of memory in use LDB: Measuring processor speeds ... Done. Info: Startup phase 6 took 0.00200009 s, 4.33594 MB of memory in use Info: CREATING 135 COMPUTE OBJECTS Info: useSync: 1 useProxySync: 0 Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 3.38813e-021 AT 11.8295 Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 5.45773e-014 AT 11.9138 Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 8.47033e-022 AT 11.9138 Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.6856e-015 AT 11.9138 Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 9.86076e-032 AT 11.8295 Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.75473e-014 AT 11.9138 Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 4.62223e-032 AT 11.9138 Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 2.12237e-015 AT 11.9138 Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 4.1359e-025 AT 11.8295 Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-015 AT 11.9138 Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 3.87741e-026 AT 11.9138 Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 5.97409e-016 AT 11.9138 Info: Startup phase 7 took 0.0179999 s, 5.01563 MB of memory in use Info: Startup phase 8 took 0.000999928 s, 5.28516 MB of memory in use Info: Finished startup at 0.284 s, 5.28516 MB of memory in use TCL: Running for 40000 steps TCL: can't read "coorList(577)": no such element in array FATAL ERROR: can't read "coorList(577)": no such element in array while executing "lindex $coorList($i) 2" (procedure "calcforces" line 5) invoked from within "calcforces" ------------- Processor 0 Exiting: Called CmiAbort ------------ Reason: FATAL ERROR: can't read "coorList(577)": no such element in array while executing "lindex $coorList($i) 2" (procedure "calcforces" line 5) invoked from within "calcforces" Charm++ fatal error: FATAL ERROR: can't read "coorList(577)": no such element in array while executing "lindex $coorList($i) 2" (procedure "calcforces" line 5) invoked from within "calcforces" This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information.