Charm++: standalone mode (not using charmrun)
Converse/Charm++ Commit ID: v6.4.0-beta1-0-g5776d21
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (8-way SMP).
Charm++> cpu topology info is gathered in 0.001 seconds.
Info: NAMD CVS-2012-06-06 for Linux-x86_64-multicore-memopt
Warning: 
Warning:        ***  EXPERIMENTAL MEMORY OPTIMIZED VERSION  ***
Warning: 
Info: 
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
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 60400 for multicore-linux64
Info: Built Thu Jun 7 13:16:22 CEST 2012 by cruzchue on Cyrus
Info: 1 NAMD  CVS-2012-06-06  Linux-x86_64-multicore-memopt  1    Cyrus  cruzchue
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0857351 s
ComputeMsmMgr:  (constructor) PE 0
Info: 35.5078 MB of memory in use based on /proc/self/stat
Info: Configuration file is eg07PSF4.namd
Info: Working in the current directory /home/cruzchue/31_runGCCX/04_INTERfile/01_small
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               1
Info: NUMBER OF STEPS        0
Info: STEPS PER CYCLE        20
Info: LOAD BALANCER  Centralized
Info: LOAD BALANCING STRATEGY  New Load Balancers -- DEFAULT
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: MIN ATOMS PER PATCH    40
Info: INITIAL TEMPERATURE    310
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC             1
Info: EXCLUDE                SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME           ./testPSF4.dcd
Info: DCD FREQUENCY          100
Info: DCD FIRST STEP         100
Info: XST FILENAME           testPSF4.xst
Info: XST FREQUENCY          100
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME        ./testPSF4
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME       ./testPSF4.restart
Info: RESTART FREQUENCY      100
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON           10
Info: SWITCHING OFF          12
Info: PAIRLIST DISTANCE      14
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                 3
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        19.5
Info: ENERGY OUTPUT STEPS    100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    1000
Info: PRESSURE OUTPUT STEPS  100
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   310
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: RANDOM NUMBER SEED     1339069947
Info: USE HYDROGEN BONDS?    NO
Info: STRUCTURE FILE         RanEctGag.psf
Info: PARAMETER file: CHARMM format! 
Info: PARAMETERS             ../99_common/par_all22_prot_cmap.inp
Info: PARAMETERS             ../99_common/par_all36_carbMOD3.prm
Info: PARAMETERS             ../99_common/toppar_all36_glycopeptideMOD3.str
Info: PARAMETERS             ../99_common/parGCCXsulf.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES     meltEct.3C35.restart.coor
In the memory optimized version, the compression of molecule information is not supported! Please use the non-memory optimized version.
FATAL ERROR: MEMOPT: unsupported usage
[0] Stack Traceback:
  [0:0] CmiAbort+0x70  [0xaf039f]
  [0:1] _Z8NAMD_diePKc+0x56  [0x541c26]
  [0:2] _ZN9NamdState24checkMemOptCompatibilityEv+0xc9  [0x97b6e9]
  [0:3] _ZN9NamdState14configListInitEP10ConfigList+0x3f1  [0x97bc01]
  [0:4]   [0x9e83bb]
  [0:5] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x34  [0x9eb034]
  [0:6] TclInvokeStringCommand+0x88  [0xb1fd88]
  [0:7]   [0xb228a0]
  [0:8]   [0xb65683]
  [0:9]   [0xb6b443]
  [0:10] TclEvalObjEx+0x86  [0xb244f6]
  [0:11]   [0xb2d44d]
  [0:12]   [0xb228a0]
  [0:13]   [0xb23c86]
  [0:14] Tcl_EvalEx+0x16  [0xb24466]
  [0:15] Tcl_FSEvalFileEx+0x151  [0xb86271]
  [0:16] Tcl_EvalFile+0x2e  [0xb8642e]
  [0:17] _ZN9ScriptTcl4loadEPc+0x1a  [0x9ec00a]
  [0:18] _Z18after_backend_initiPPc+0x24a  [0x54653a]
  [0:19] main+0x1a  [0x50bb5a]
  [0:20] __libc_start_main+0xed  [0x7fd0340c076d]
  [0:21]   [0x50dd2d]
[0] Stack Traceback:
  [0:0]   [0xaef8cc]
  [0:1] CmiAbort+0xaa  [0xaf03d9]
  [0:2] _Z8NAMD_diePKc+0x56  [0x541c26]
  [0:3] _ZN9NamdState24checkMemOptCompatibilityEv+0xc9  [0x97b6e9]
  [0:4] _ZN9NamdState14configListInitEP10ConfigList+0x3f1  [0x97bc01]
  [0:5]   [0x9e83bb]
  [0:6] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x34  [0x9eb034]
  [0:7] TclInvokeStringCommand+0x88  [0xb1fd88]
  [0:8]   [0xb228a0]
  [0:9]   [0xb65683]
  [0:10]   [0xb6b443]
  [0:11] TclEvalObjEx+0x86  [0xb244f6]
  [0:12]   [0xb2d44d]
  [0:13]   [0xb228a0]
  [0:14]   [0xb23c86]
  [0:15] Tcl_EvalEx+0x16  [0xb24466]
  [0:16] Tcl_FSEvalFileEx+0x151  [0xb86271]
  [0:17] Tcl_EvalFile+0x2e  [0xb8642e]
  [0:18] _ZN9ScriptTcl4loadEPc+0x1a  [0x9ec00a]
  [0:19] _Z18after_backend_initiPPc+0x24a  [0x54653a]
  [0:20] main+0x1a  [0x50bb5a]
  [0:21] __libc_start_main+0xed  [0x7fd0340c076d]
  [0:22]   [0x50dd2d]