apoa1/ apoa1/apoa1.pdb apoa1/apoa1.psf apoa1/par_all22_prot_lipid.xplor apoa1/par_all22_popc.xplor apoa1/apoa1.namd Charm++> Running on MPI version: 3.0 Charm++> level of thread support used: MPI_THREAD_SINGLE (desired: MPI_THREAD_SINGLE) Charm++> Running in non-SMP mode: numPes 23 Charm++> Using recursive bisection (scheme 3) for topology aware partitions Converse/Charm++ Commit ID: v6.6.1-rc1-1-gba7c3c3-namd-charm-6.6.1-build-2014-Dec-08-28969 Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'. CharmLB> Load balancer assumes all CPUs are same. Charm++> Running on 1 unique compute nodes (48-way SMP). Charm++> cpu topology info is gathered in 0.010 seconds. Info: NAMD 2.10 for Linux-x86_64-MPI 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 60601 for mpi-linux-x86_64-ifort-mpicxx Info: Built Mon Jul 27 15:39:43 IST 2015 by puneet on shavak249 Info: 1 NAMD 2.10 Linux-x86_64-MPI 23 shavak249 puneet Info: Running on 23 processors, 23 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.030926 s Info: 290.902 MB of memory in use based on /proc/self/stat Info: Configuration file is ./apoa1/apoa1.namd Info: Changed directory to ./apoa1 TCL: Suspending until startup complete. Info: SIMULATION PARAMETERS: Info: TIMESTEP 1 Info: NUMBER OF STEPS 500 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 108.861 0 0 Info: PERIODIC CELL BASIS 2 0 108.861 0 Info: PERIODIC CELL BASIS 3 0 0 77.758 Info: PERIODIC CELL CENTER 0 0 0 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: PME BACKGROUND SCALING 1 Info: MIN ATOMS PER PATCH 40 Info: INITIAL TEMPERATURE 300 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: NO DCD TRAJECTORY OUTPUT Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT Info: NO VELOCITY DCD OUTPUT Info: NO FORCE DCD OUTPUT Info: OUTPUT FILENAME /usr/tmp/apoa1-out 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 13.5 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 16 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 20 Info: PARTICLE MESH EWALD (PME) ACTIVE Info: PME TOLERANCE 1e-06 Info: PME EWALD COEFFICIENT 0.257952 Info: PME INTERPOLATION ORDER 4 Info: PME GRID DIMENSIONS 108 108 80 Info: PME MAXIMUM GRID SPACING 1.5 Info: Attempting to read FFTW data from FFTW_NAMD_2.10_Linux-x86_64-MPI.txt Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done. Info: Writing FFTW data to FFTW_NAMD_2.10_Linux-x86_64-MPI.txt Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 4 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 74269 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB apoa1.pdb Info: STRUCTURE FILE apoa1.psf Info: PARAMETER file: XPLOR format! (default) Info: PARAMETERS par_all22_prot_lipid.xplor Info: PARAMETERS par_all22_popc.xplor Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: SUMMARY OF PARAMETERS: Info: 177 BONDS Info: 435 ANGLES Info: 446 DIHEDRAL Info: 45 IMPROPER Info: 0 CROSSTERM Info: 83 VDW Info: 6 VDW_PAIRS Info: 0 NBTHOLE_PAIRS Info: TIME FOR READING PSF FILE: 1.02327 Info: TIME FOR READING PDB FILE: 0.130059 Info: Info: **************************** Info: STRUCTURE SUMMARY: Info: 92224 ATOMS Info: 70660 BONDS Info: 74136 ANGLES Info: 74130 DIHEDRALS Info: 1402 IMPROPERS Info: 0 CROSSTERMS Info: 0 EXCLUSIONS Info: 1568 DIHEDRALS WITH MULTIPLE PERIODICITY (BASED ON PSF FILE) Info: 276669 DEGREES OF FREEDOM Info: 32992 HYDROGEN GROUPS Info: 4 ATOMS IN LARGEST HYDROGEN GROUP Info: 32992 MIGRATION GROUPS Info: 4 ATOMS IN LARGEST MIGRATION GROUP Info: TOTAL MASS = 553785 amu Info: TOTAL CHARGE = -14 e Info: MASS DENSITY = 0.997951 g/cm^3 Info: ATOM DENSITY = 0.100081 atoms/A^3 Info: ***************************** Info: Info: Entering startup at 32.2657 s, 413.086 MB of memory in use Info: Startup phase 0 took 0.000956059 s, 413.086 MB of memory in use Info: ADDED 218698 IMPLICIT EXCLUSIONS Info: Startup phase 1 took 0.177169 s, 435.109 MB of memory in use Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556 Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556 Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946 Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946 Info: Startup phase 2 took 0.00177193 s, 435.109 MB of memory in use Info: Startup phase 3 took 0.00086689 s, 435.109 MB of memory in use Info: Startup phase 4 took 0.00143814 s, 435.109 MB of memory in use Info: Startup phase 5 took 0.000895023 s, 435.109 MB of memory in use Info: PATCH GRID IS 6 (PERIODIC) BY 6 (PERIODIC) BY 4 (PERIODIC) Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY Info: REMOVING COM VELOCITY 0.00117959 0.0289175 0.0202933 Info: LARGEST PATCH (56) HAS 718 ATOMS Info: TORUS A SIZE 23 USING 0 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0.0327508 s, 453.512 MB of memory in use Info: PME using 22 and 22 processors for FFT and reciprocal sum. Info: PME GRID LOCATIONS: 1 2 3 4 5 6 7 8 9 10 ... Info: PME TRANS LOCATIONS: 1 2 3 4 5 6 7 8 9 10 ... Info: PME USING 22 GRID NODES AND 22 TRANS NODES Info: Startup phase 7 took 0.00365806 s, 454.02 MB of memory in use Info: Startup phase 8 took 0.00569391 s, 459.098 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0.00113821 s, 459.098 MB of memory in use Info: CREATING 2995 COMPUTE OBJECTS Info: Startup phase 10 took 0.00198698 s, 459.098 MB of memory in use Info: useSync: 1 useProxySync: 0 Info: Startup phase 11 took 0.000846863 s, 459.098 MB of memory in use Info: Startup phase 12 took 0.000128031 s, 459.098 MB of memory in use Info: Finished startup at 32.495 s, 459.098 MB of memory in use ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY: 0 12352.4560 14603.1480 4549.0710 48.1064 -362073.7644 24229.5343 0.0000 0.0000 82752.2738 -223539.1750 301.0300 -306291.4488 -223524.8476 301.0300 -2568.6725 -3582.2555 921491.4634 -2568.6725 -3582.2555 ENERGY: 1 18844.4109 15785.9133 4571.2456 53.5350 -361670.8138 24319.4022 0.0000 0.0000 75223.8495 -222872.4573 273.6437 -298096.3068 -223478.1937 273.6437 -3192.4049 -3497.3102 921491.4634 -3192.4049 -3497.3102 ENERGY: 2 29488.6214 18758.6024 4637.0922 69.5538 -360338.7682 24512.0178 0.0000 0.0000 61082.0538 -221790.8268 222.1997 -282872.8806 -223476.2577 222.1997 -4269.6708 -3354.1998 921491.4634 -4269.6708 -3354.1998 ENERGY: 3 29918.6891 22271.8869 4734.9573 94.3383 -358090.2897 24689.8970 0.0000 0.0000 54714.9832 -221665.5378 199.0381 -276380.5211 -223477.2859 199.0381 -4381.8243 -3200.6936 921491.4634 -4381.8243 -3200.6936 ----------- ENERGY: 500 20974.8940 19756.6576 5724.4523 179.8271 -337741.4197 23251.1008 0.0000 0.0000 45359.0786 -222495.4093 165.0039 -267854.4878 -222061.0911 165.0039 -3197.5170 -2425.4142 921491.4634 -3197.5170 -2425.4142 WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 500 WRITING COORDINATES TO OUTPUT FILE AT STEP 500 The last position output (seq=-2) takes 0.002 seconds, 463.621 MB of memory in use WRITING VELOCITIES TO OUTPUT FILE AT STEP 500 The last velocity output (seq=-2) takes 0.002 seconds, 463.621 MB of memory in use ==================================================== WallClock: 66.561104 CPUTime: 66.561104 Memory: 463.621094 MB (namd_build.sh)