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 0.013 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 0.0150001 s
Info: 3.22656 MB of memory in use based on GetProcessMemoryInfo
Info: Configuration file is NSD1-SET-Crystalstructure-original-nowater_autopsf-solvate-namd.namd
Info: Working in the current directory D:\Program Files\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    298
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           NSD1-SET-Crystalstructure-original-nowater_autopsf-solvate-namd.dcd
Info: DCD FREQUENCY          50
Info: DCD FIRST STEP         50
Info: XST FILENAME           NSD1-SET-Crystalstructure-original-nowater_autopsf-solvate-namd.xst
Info: XST FREQUENCY          50
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME        NSD1-SET-Crystalstructure-original-nowater_autopsf-solvate-namd
Info: RESTART FILENAME       NSD1-SET-Crystalstructure-original-nowater_autopsf-solvate-namd.restart
Info: RESTART FREQUENCY      1000
Info: SWITCHING ACTIVE
Info: SWITCHING ON           9
Info: SWITCHING OFF          10
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: ENERGY OUTPUT STEPS    100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    1000
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   298
Info: LANGEVIN DAMPING COEFFICIENT IS 1 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     12345
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         NSD1-SET-Crystalstructure-original-nowater_autopsf-solvate.pdb
Info: STRUCTURE FILE         NSD1-SET-Crystalstructure-original-nowater_autopsf-solvate.psf
Info: PARAMETER file: CHARMM format! 
Info: PARAMETERS             D:/Program Files/University of Illinois/VMD/plugins/noarch/tcl/readcharmmpar1.2/par_all27_prot_lipid_na.inp
Info: PARAMETERS             C:/Users/Daan/Documents/PhD-KNU/Correct-AdoMet/AdoMet-paper-parameters-auto.par
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
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE C:/Users/Daan/Documents/PhD-KNU/Correct-AdoMet/AdoMet-paper-parameters-auto.par
LINE=*CN8B S 240.000 1.858 !hms: r0 from QM(aq)*