#############| NAMD |############### Charm++> Running on MPI version: 3.0 Charm++> level of thread support used: MPI_THREAD_FUNNELED (desired: MPI_THREAD_FUNNELED) Charm++> Running in SMP mode: numNodes 1, 23 worker threads per process Charm++> The comm. thread both sends and receives messages 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 0.003 seconds. Info: NAMD 2.10 for Linux-x86_64-MPI-smp 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-smp-mpicxx Info: Built Mon Jul 27 10:41:25 IST 2015 by puneet on shavak249 Info: 1 NAMD 2.10 Linux-x86_64-MPI-smp 23 shavak249 puneet Info: Running on 23 processors, 1 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.0481691 s Info: 1600.52 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 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-smp.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-smp.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: 2.75224 Info: TIME FOR READING PDB FILE: 1.18482 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 4.07148 s, 1697.09 MB of memory in use Info: Startup phase 0 took 0.00229907 s, 1697.09 MB of memory in use Info: ADDED 218698 IMPLICIT EXCLUSIONS Info: Startup phase 1 took 0.47669 s, 1697.09 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 0.00525904 s, 1697.09 MB of memory in use Info: Startup phase 3 took 0.00245094 s, 1697.09 MB of memory in use Info: Startup phase 4 took 0.00844121 s, 1697.09 MB of memory in use Info: Startup phase 5 took 0.00198197 s, 1697.09 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 0.164607 s, 1761.09 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 1 GRID NODES AND 1 TRANS NODES Info: Startup phase 7 took 0.00711083 s, 1761.09 MB of memory in use Info: Startup phase 8 took 0.00574899 s, 1761.09 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0.00673199 s, 1761.09 MB of memory in use Info: CREATING 2995 COMPUTE OBJECTS Info: useSync: 1 useProxySync: 0 Info: Startup phase 10 took 0.0805361 s, 1761.09 MB of memory in use Info: Startup phase 11 took 0.00224996 s, 1761.09 MB of memory in use Info: Startup phase 12 took 0.000500917 s, 1761.09 MB of memory in use Info: Finished startup at 4.83609 s, 1761.09 MB of memory in use ERROR: Atom 27216 velocity is -10752.9 1207.92 -5988.05 (limit is 12000, atom 268 of 667 on patch 64 pe 18) ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on patch 64 pe 18). ERROR: Atom 348 velocity is 41449.5 -24143.2 -4526.39 (limit is 12000, atom 3 of 604 on patch 65 pe 20) ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on patch 65 pe 20). ERROR: Atom 20231 velocity is 17243 23838.3 -1832.79 (limit is 12000, atom 183 of 637 on patch 14 pe 8) ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on patch 14 pe 8). 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 -362073.7645 -127660.4690 0.0000 0.0000 82752.2738 -375429.1785 301.0300 -458181.4522 12464127.1863 301.0300 4263437.1823 4107551.8235 921491.4634 4263437.1823 4107551.8235 ERROR: Exiting prematurely; see error messages above. ==================================================== WallClock: 5.376962 CPUTime: 5.191210 Memory: 1761.085938 MB