Charm++: standalone mode (not using charmrun)
Charm++> scheduler running in netpoll mode.
Charm++> Running on 1 unique compute nodes (8-way SMP).
Charm++> cpu topology info is gathered in 0.000 seconds.
Info: NAMD CVS-2012-01-18 for Linux-x86_64
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 60303 for net-linux-x86_64-iccstatic
Info: Built Wed Jan 18 02:17:25 CST 2012 by jim on lisboa.ks.uiuc.edu
Info: 1 NAMD  CVS-2012-01-18  Linux-x86_64  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 0.017719 s
Info: 1.50191 MB of memory in use based on CmiMemoryUsage
Info: Configuration file is v01.MinProtPSF.namd
Info: Working in the current directory /home/cruzchue/31_runGCCX/01_1dimer
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               2
Info: NUMBER OF STEPS        0
Info: STEPS PER CYCLE        10
Info: PERIODIC CELL BASIS 1  307.571 0 0
Info: PERIODIC CELL BASIS 2  153.78 267.183 0
Info: PERIODIC CELL BASIS 3  0 0 815
Info: PERIODIC CELL CENTER   0 0 0
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING TO IMAGE NEAREST TO PERIODIC CELL CENTER.
Info: LOAD BALANCER  Centralized
Info: LOAD BALANCING STRATEGY  New Load Balancers -- DEFAULT
Info: LDB PERIOD             2000 steps
Info: FIRST LDB TIMESTEP     50
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           v01.MinProt.dcd
Info: DCD FREQUENCY          1
Info: DCD FIRST STEP         1
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME           v01.MinProt.xst
Info: XST FREQUENCY          1
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME        v01.MinProt
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME       v01.MinProt.restart
Info: RESTART FREQUENCY      1
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: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    50
Info: PRESSURE OUTPUT STEPS  1
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : ALL
Info:         ERROR TOLERANCE : 1e-08
Info:          MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED     1339059456
Info: USE HYDROGEN BONDS?    NO
Info: STRUCTURE FILE         v01.psf
Info: PARAMETER file: CHARMM format! 
Info: PARAMETERS             ../99_common/par_all22_prot_cmap.inp
Info: PARAMETERS             ../99_common/par_all32_lipid.prm
Info: PARAMETERS             ../99_common/par_all36_carbMOD3.prm
Info: BINARY COORDINATES     v01.coor
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SUMMARY OF PARAMETERS:
Info: 348 BONDS
Info: 941 ANGLES
Info: 2110 DIHEDRAL
Info: 65 IMPROPER
Info: 6 CROSSTERM
Info: 194 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PSF FILE: 34.5907