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 0.011 seconds.
Info: NAMD 2.9b2 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 Mar 26 15:11:37 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 0.0139999 s
Info: 3.24609 MB of memory in use based on GetProcessMemoryInfo
Info: Configuration file is adk-step1.namd
Info: Working in the current directory C:\Program Files (x86)\University of Illinois\VMD
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    300
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC             80
Info: EXCLUDE                SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME           adk-step1.dcd
Info: DCD FREQUENCY          1000
Info: DCD FIRST STEP         1000
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME        adk-step1
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME       adk-step1.restart
Info: RESTART FREQUENCY      1000
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON           9
Info: SWITCHING OFF          10
Info: PAIRLIST DISTANCE      11
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        13.5
Info: ENERGY OUTPUT STEPS    100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    1000
Info: PRESSURE OUTPUT STEPS  100
Info: GRID FORCE ACTIVE
Info:  Please include this reference in published work using
Info:  the Gridforce module of NAMD: David Wells, Volha Abramkina,
Info:  and Aleksei Aksimentiev, J. Chem. Phys. 127:125101-10 (2007).
Info: MGRIDFORCE key BaseGridForceParams
Info:            Potfile 4ake-target_autopsf-grid.dx
Info:            Scale 0.3 0.3 0.3
Info:            File 1ake-initial_autopsf-grid.pdb
Info:            Col O
Info:            ChargeCol B
Info:            VOffset 0 0 0
Info:            Continuous K1 FALSE
Info:            Continuous K2 FALSE
Info:            Continuous K3 FALSE
Info:            Volts FALSE
Info:            Gridforce-Lite FALSE
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: RIGID BONDS TO HYDROGEN : WATER
Info:         ERROR TOLERANCE : 1e-008
Info:          MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: NONBONDED FORCES EVALUATED EVERY 2 STEPS
Info: RANDOM NUMBER SEED     1333615608
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         D:/tmp/1ake-initial_autopsf-docked.pdb
Info: STRUCTURE FILE         1ake-initial_autopsf.psf
Info: PARAMETER file: CHARMM format! 
Info: PARAMETERS             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
Info: TIME FOR READING PSF FILE: 0.309
Info: READING EXTRA BONDS FILE 1ake-extrabonds.txt
Info: READING EXTRA BONDS FILE 1ake-extrabonds-cispeptide.txt
Info: READING EXTRA BONDS FILE 1ake-extrabonds-chirality.txt
Info: READ 80 EXTRA BONDS
Info: READ 80 EXTRA ANGLES
Info: READ 493 EXTRA DIHEDRALS
Info: READ 438 EXTRA IMPROPERS
Info: TIME FOR READING PDB FILE: 0.0139999
Info: 
FATAL ERROR: Grid force potential file incorrectly formatted