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)*