Charm++: standalone mode (not using charmrun)
Charm++ warning> fences and atomic operations not available in native assembly
Converse/Charm++ Commit ID: v6.4.0-beta1-0-g5776d21
[0] isomalloc.c> Disabling isomalloc because mmap() does not work
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (4-way SMP).
Charm++> cpu topology info is gathered in 0.016 seconds.
Info: NAMD 2.9 for Win32-multicore
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-win32
Info: Built Mon Apr 30 14:10:39 CDT 2012 by jcphill on honor
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0159998 s
Info: 2.48828 MB of memory in use based on GetProcessMemoryInfo
Info: Configuration file is namd-temp.namd
Info: Working in the current directory F:\Dropbox\NAMDEnergy
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               1
Info: NUMBER OF STEPS        1
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    0
Info: CENTER OF MASS MOVING INITIALLY? YES
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: NO DCD TRAJECTORY OUTPUT
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME        namd-temp
Info: BINARY OUTPUT FILES WILL BE USED
Info: NO RESTART FILE
Info: SWITCHING ACTIVE
Info: SWITCHING ON           10
Info: SWITCHING OFF          12
Info: PAIRLIST DISTANCE      12
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        14.5
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    100
Info: PAIR INTERACTION CALCULATIONS ACTIVE
Info: USING FLAG 1 FOR GROUP 1
Info: USING FLAG 2 FOR GROUP 2
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     1423732190
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         namd-temp.pdb
Info: STRUCTURE FILE         IL219-Mixed.psf
Info: PARAMETER file: CHARMM format! 
Info: PARAMETERS             C:/Program Files (x86)/University of Illinois/VMD/plugins/noarch/tcl/readcharmmpar1.2/par_all27_prot_lipid_na.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS

Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2
PREVIOUS VALUES  k=130  theta0=107.5 k_ub=0 r_ub=0
   USING VALUES  k=130  theta0=107 k_ub=0 r_ub=0
Info: SUMMARY OF PARAMETERS:
Info: 307 BONDS
Info: 769 ANGLES
Info: 1254 DIHEDRAL
Info: 81 IMPROPER
Info: 6 CROSSTERM
Info: 190 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CR