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