Charm++: standalone mode (not using charmrun) Charm++> Running in Multicore mode: 20 threads (PEs) Charm++> Using recursive bisection (scheme 3) for topology aware partitions Converse/Charm++ Commit ID: v6.10.2-0-g7bf00fa-namd-charm-6.10.2-build-2020-Aug-05-556 Warning> Randomization of virtual memory (ASLR) is turned on in the kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try running with '+isomalloc_sync'. CharmLB> Load balancer assumes all CPUs are same. Charm++> Running on 1 hosts (1 sockets x 20 cores x 1 PUs = 20-way SMP) Charm++> cpu topology info is gathered in 0.005 seconds. Info: NAMD Git-2020-08-16 for Linux-x86_64-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. Chem. Phys. 153:044130 (2020) doi:10.1063/5.0014475 Info: in all publications reporting results obtained with NAMD. Info: Info: Based on Charm++/Converse 61002 for multicore-linux-x86_64-iccstatic Info: Built Sun Aug 16 02:09:50 CDT 2020 by jim on belfast.ks.uiuc.edu Info: 1 NAMD Git-2020-08-16 Linux-x86_64-multicore 20 am-VirtualBox am Info: Running on 20 processors, 1 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.0946374 s CkLoopLib is used in SMP with simple dynamic scheduling (converse-level notification) Info: 1398.27 MB of memory in use based on /proc/self/stat Info: Configuration file is nvt.namd Info: Working in the current directory /home/MD/usb TCL: Suspending until startup complete. Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 Info: NUMBER OF STEPS 0 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 79.187 0 0 Info: PERIODIC CELL BASIS 2 0 89.868 0 Info: PERIODIC CELL BASIS 3 0 0 96.955 Info: PERIODIC CELL CENTER 126.523 357.63 103.735 Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT. Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT. 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: VELOCITY FILE minimize.restart.vel 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 nvt.dcd Info: DCD FREQUENCY 1000 Info: DCD FIRST STEP 1000 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME nvt.xst Info: XST FREQUENCY 1000 Info: NO VELOCITY DCD OUTPUT Info: NO FORCE DCD OUTPUT Info: OUTPUT FILENAME nvt Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME nvt.restart Info: RESTART FREQUENCY 1000 Info: BINARY RESTART FILES WILL BE USED Info: SWITCHING ACTIVE Info: SWITCHING ON 10 Info: SWITCHING OFF 12 Info: PAIRLIST DISTANCE 14 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 0.495 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 16.995 Info: ENERGY OUTPUT STEPS 1000 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 1000 Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 310 Info: LANGEVIN USING BBK INTEGRATOR Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS Warning: Option useGroupPressure is being enabled due to pressure control with rigidBonds. Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE Info: TARGET PRESSURE IS 1.01325 BAR Info: OSCILLATION PERIOD IS 100 FS Info: DECAY TIME IS 50 FS Info: PISTON TEMPERATURE IS 310 K Info: PRESSURE CONTROL IS GROUP-BASED Info: INITIAL STRAIN RATE IS 0 0 0 Info: CELL FLUCTUATION IS ISOTROPIC 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 80 96 108 Info: PME MAXIMUM GRID SPACING 1 Info: Attempting to read FFTW data from FFTW_NAMD_Git-2020-08-16_Linux-x86_64-multicore.txt Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done. Info: Writing FFTW data to FFTW_NAMD_Git-2020-08-16_Linux-x86_64-multicore.txt Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 2 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 : ALL Info: ERROR TOLERANCE : 1e-08 Info: MAX ITERATIONS : 100 Info: RIGID WATER USING SETTLE ALGORITHM Info: RANDOM NUMBER SEED 1597642909 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB solvate.pdb Info: STRUCTURE FILE solvate.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS par_all36_prot.prm Info: PARAMETERS par_all36m_prot.prm Info: PARAMETERS par_all36_carb.prm Info: PARAMETERS par_all36_lipid.prm Info: PARAMETERS par_all36_cgenff.prm Info: PARAMETERS par_all36_na.prm Info: PARAMETERS par_interface.prm Info: PARAMETERS unk.prm Info: PARAMETERS toppar_water_ions.mod.str Info: PARAMETERS toppar_ions_won.str Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: BINARY COORDINATES minimize.restart.coor Warning: DUPLICATE ANGLE ENTRY FOR CD-CT2-NH2 PREVIOUS VALUES k=52 theta0=108 k_ub=0 r_ub=0 USING VALUES k=50 theta0=107 k_ub=0 r_ub=0 Warning: DUPLICATE ANGLE ENTRY FOR CD-CT2-NH2 PREVIOUS VALUES k=50 theta0=107 k_ub=0 r_ub=0 USING VALUES k=52 theta0=108 k_ub=0 r_ub=0 Warning: DUPLICATE CMAP ENTRY FOR C-NH1-CT1-C NH1-CT1-C-NH1, USING NEW VALUES Warning: DUPLICATE CMAP ENTRY FOR C-NH1-CT1-C NH1-CT1-C-N, USING NEW VALUES Info: SKIPPING rtf SECTION IN STREAM FILE Info: SUMMARY OF PARAMETERS: Info: 1218 BONDS Info: 3519 ANGLES Info: 8284 DIHEDRAL Info: 236 IMPROPER Info: 12 CROSSTERM Info: 546 VDW Info: 78 VDW_PAIRS Info: 0 NBTHOLE_PAIRS Info: TIME FOR READING PSF FILE: 26.9455 Info: Reading pdb file solvate.pdb Info: TIME FOR READING PDB FILE: 0.864896 Info: Info: **************************** Info: STRUCTURE SUMMARY: Info: 63380 ATOMS Info: 45494 BONDS Info: 35116 ANGLES Info: 25174 DIHEDRALS Info: 1560 IMPROPERS Info: 575 CROSSTERMS Info: 0 EXCLUSIONS Info: 58662 RIGID BONDS Info: 131478 DEGREES OF FREEDOM Info: 22736 HYDROGEN GROUPS Info: 4 ATOMS IN LARGEST HYDROGEN GROUP Info: 22736 MIGRATION GROUPS Info: 4 ATOMS IN LARGEST MIGRATION GROUP Info: TOTAL MASS = 391769 amu Info: TOTAL CHARGE = -18 e Info: MASS DENSITY = 0.942889 g/cm^3 Info: ATOM DENSITY = 0.0918593 atoms/A^3 Info: ***************************** Info: Reading from binary file minimize.restart.coor Info: Info: Entering startup at 32.8787 s, 1441.53 MB of memory in use Info: Startup phase 0 took 0.0456589 s, 1441.53 MB of memory in use Info: ADDED 105247 IMPLICIT EXCLUSIONS Info: Startup phase 1 took 0.296097 s, 1452.82 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: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 4.59334e-32 AT 11.9974 Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 7.4108e-17 AT 11.9974 Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946 Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 1.53481e-26 AT 11.9974 Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.96691e-18 AT 11.9974 Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946 Info: Startup phase 2 took 0.136242 s, 1460.24 MB of memory in use Info: Startup phase 3 took 0.0411011 s, 1460.24 MB of memory in use Info: Startup phase 4 took 0.0626279 s, 1460.73 MB of memory in use Info: Startup phase 5 took 0.0444754 s, 1460.73 MB of memory in use Info: PATCH GRID IS 4 (PERIODIC) BY 5 (PERIODIC) BY 5 (PERIODIC) Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY Info: Reading from binary file minimize.restart.vel Info: REMOVING COM VELOCITY 0.00698684 0.0345861 0.026809 Info: LARGEST PATCH (30) HAS 741 ATOMS Info: TORUS A SIZE 1 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 0.227912 s, 1473.08 MB of memory in use Info: PME using 20 and 20 processors for FFT and reciprocal sum. Info: PME GRID LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ... Info: PME TRANS LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ... Info: PME USING 1 GRID NODES AND 1 TRANS NODES Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done. Info: Startup phase 7 took 0.0308286 s, 1473.08 MB of memory in use Info: Startup phase 8 took 0.0252558 s, 1473.08 MB of memory in use Info: Startup phase 9 took 0.000338966 s, 1473.08 MB of memory in use Info: Startup phase 10 took 0.000261421 s, 1473.08 MB of memory in use Info: Startup phase 11 took 0.0674748 s, 1473.08 MB of memory in use LDB: Central LB being created... Info: Startup phase 12 took 0.0844878 s, 1473.08 MB of memory in use Info: CREATING 2100 COMPUTE OBJECTS Info: useSync: 0 useProxySync: 0 Info: Startup phase 13 took 0.0954997 s, 1473.08 MB of memory in use Info: Startup phase 14 took 0.0436662 s, 1473.08 MB of memory in use Info: Startup phase 15 took 0.00813187 s, 1473.08 MB of memory in use Info: Finished startup at 34.0888 s, 1473.08 MB of memory in use REINITIALIZING VELOCITIES AT STEP 0 TO 310 KELVIN. TCL: Running for 250000 steps ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY: 0 2015.8204 5734.2718 5996.2482 304.5469 -204530.0189 15235.4931 0.0000 0.0000 40489.9251 -134753.7134 309.9447 -175243.6385 -134598.9820 309.9447 321.7523 351.0155 689968.5266 321.7523 351.0155 OPENING EXTENDED SYSTEM TRAJECTORY FILE LDB: ============= START OF LOAD BALANCING ============== 38.129 LDB: ============== END OF LOAD BALANCING =============== 38.1404 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 38.1868 LDB: ============= START OF LOAD BALANCING ============== 49.326 LDB: Largest compute 113 load 0.546953 is 8.1% of average load 6.770205 LDB: Average compute 0.059596 is 0.9% of average load 6.770205 LDB: Partitioning computes with target load 0.677020 LDB: Increased migratable compute count from 1900 to 1900 LDB: Largest unpartitionable compute is 0.074561 LDB: ============== END OF LOAD BALANCING =============== 49.3313 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 49.3345 Info: Initial time: 20 CPUs 0.138188 s/step 0.799699 days/ns 1484.3 MB memory LDB: ============= START OF LOAD BALANCING ============== 51.3625 LDB: ============== END OF LOAD BALANCING =============== 51.363 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 51.3635 LDB: ============= START OF LOAD BALANCING ============== 60.8711 LDB: Largest compute 129 load 0.548964 is 8.2% of average load 6.696984 LDB: Average compute 0.059488 is 0.9% of average load 6.696984 LDB: TIME 60.8779 LOAD: AVG 6.69698 MAX 8.38628 PROXIES: TOTAL 340 MAXPE 19 MAXPATCH 5 None MEM: 1484.99 MB LDB: TIME 60.8845 LOAD: AVG 6.69698 MAX 6.89694 PROXIES: TOTAL 340 MAXPE 19 MAXPATCH 5 TorusLB MEM: 1484.99 MB LDB: ============== END OF LOAD BALANCING =============== 60.8893 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 60.8947 Info: Initial time: 20 CPUs 0.115819 s/step 0.670249 days/ns 1485.86 MB memory LDB: ============= START OF LOAD BALANCING ============== 70.8339 LDB: Largest compute 149 load 0.680361 is 8.3% of average load 8.200556 LDB: Average compute 0.073128 is 0.9% of average load 8.200556 LDB: TIME 70.8383 LOAD: AVG 8.20056 MAX 8.93115 PROXIES: TOTAL 340 MAXPE 19 MAXPATCH 5 None MEM: 1485.86 MB LDB: TIME 70.84 LOAD: AVG 8.20056 MAX 8.93115 PROXIES: TOTAL 340 MAXPE 19 MAXPATCH 5 RefineTorusLB MEM: 1485.86 MB LDB: TIME 70.8454 LOAD: AVG 8.20056 MAX 8.36685 PROXIES: TOTAL 340 MAXPE 19 MAXPATCH 5 RefineTorusLB MEM: 1485.86 MB LDB: ============== END OF LOAD BALANCING =============== 70.8465 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 70.8495 Info: Initial time: 20 CPUs 0.0986415 s/step 0.570842 days/ns 1485.86 MB memory LDB: ============= START OF LOAD BALANCING ============== 79.7098 LDB: Largest compute 134 load 0.643594 is 7.9% of average load 8.141362 LDB: Average compute 0.072614 is 0.9% of average load 8.141362 LDB: TIME 79.7147 LOAD: AVG 8.14136 MAX 8.60437 PROXIES: TOTAL 340 MAXPE 19 MAXPATCH 5 None MEM: 1485.86 MB LDB: TIME 79.7161 LOAD: AVG 8.14136 MAX 8.60437 PROXIES: TOTAL 340 MAXPE 19 MAXPATCH 5 RefineTorusLB MEM: 1485.86 MB LDB: TIME 79.7193 LOAD: AVG 8.14136 MAX 8.30636 PROXIES: TOTAL 340 MAXPE 19 MAXPATCH 5 RefineTorusLB MEM: 1485.86 MB LDB: ============== END OF LOAD BALANCING =============== 79.7209 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 79.7228 Info: Benchmark time: 20 CPUs 0.0886525 s/step 0.513036 days/ns 1485.86 MB memory Info: Benchmark time: 20 CPUs 0.0854121 s/step 0.494283 days/ns 1485.86 MB memory Info: Benchmark time: 20 CPUs 0.0870429 s/step 0.503721 days/ns 1485.86 MB memory Info: Benchmark time: 20 CPUs 0.0872981 s/step 0.505197 days/ns 1485.86 MB memory Info: Benchmark time: 20 CPUs 0.0871154 s/step 0.50414 days/ns 1485.86 MB memory Info: Benchmark time: 20 CPUs 0.0883806 s/step 0.511462 days/ns 1485.86 MB memory TIMING: 1000 CPU: 95.1539, 0.0945417/step Wall: 98.4559, 0.0967415/step, 6.69129 hours remaining, 1488.664062 MB of memory in use. ENERGY: 1000 2040.4821 5598.0800 6014.5263 308.8408 -208619.5824 14499.5890 0.0000 0.0000 42112.9090 -138045.1552 322.3685 -180158.0642 -137887.6279 323.2802 -146.8835 -119.4699 645403.4322 -3.3166 -3.3460 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1000 OPENING COORDINATE DCD FILE WRITING COORDINATES TO DCD FILE nvt.dcd AT STEP 1000 WRITING COORDINATES TO RESTART FILE AT STEP 1000 FINISHED WRITING RESTART COORDINATES The last position output (seq=1000) takes 0.022 seconds, 1488.664 MB of memory in use WRITING VELOCITIES TO RESTART FILE AT STEP 1000 FINISHED WRITING RESTART VELOCITIES The last velocity output (seq=1000) takes 0.006 seconds, 1490.840 MB of memory in use TIMING: 2000 CPU: 191.691, 0.0965376/step Wall: 195.632, 0.0971756/step, 6.69432 hours remaining, 1490.839844 MB of memory in use. ENERGY: 2000 1999.7511 5741.4918 5995.0804 343.9299 -211478.1070 15020.3166 0.0000 0.0000 41488.4052 -140889.1320 317.5880 -182377.5372 -140729.4356 319.7471 -25.1524 9.2033 630502.3933 0.4594 0.3979 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 2000 WRITING COORDINATES TO DCD FILE nvt.dcd AT STEP 2000 WRITING COORDINATES TO RESTART FILE AT STEP 2000 FINISHED WRITING RESTART COORDINATES The last position output (seq=2000) takes 0.021 seconds, 1490.840 MB of memory in use WRITING VELOCITIES TO RESTART FILE AT STEP 2000 FINISHED WRITING RESTART VELOCITIES The last velocity output (seq=2000) takes 0.007 seconds, 1491.301 MB of memory in use WRITING COORDINATES TO DCD FILE nvt.dcd AT STEP 3000 WRITING COORDINATES TO RESTART FILE AT STEP 3000 FINISHED WRITING RESTART COORDINATES The last position output (seq=3000) takes 0.017 seconds, 1491.301 MB of memory in use WRITING VELOCITIES TO RESTART FILE AT STEP 3000 FINISHED WRITING RESTART VELOCITIES The last velocity output (seq=3000) takes 0.006 seconds, 1491.301 MB of memory in use TIMING: 3000 CPU: 293.133, 0.101441/step Wall: 297.149, 0.101518/step, 6.96525 hours remaining, 1491.300781 MB of memory in use. ENERGY: 3000 2014.6248 5631.7136 6022.6273 316.2571 -212591.2861 15142.0490 0.0000 0.0000 40936.8785 -142527.1358 313.3661 -183464.0143 -142375.6753 315.3864 51.0289 81.8662 627439.9916 -1.5097 -1.5190 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 3000 TIMING: 4000 CPU: 393.001, 0.0998685/step Wall: 397.77, 0.10062/step, 6.87573 hours remaining, 1491.300781 MB of memory in use. ENERGY: 4000 2059.3951 5708.3431 5946.2449 348.8964 -213580.8310 15426.4258 0.0000 0.0000 40844.4377 -143247.0880 312.6585 -184091.5258 -143096.9318 312.8068 54.9446 79.6348 628037.9658 4.3289 4.3550 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 4000 WRITING COORDINATES TO DCD FILE nvt.dcd AT STEP 4000 WRITING COORDINATES TO RESTART FILE AT STEP 4000 FINISHED WRITING RESTART COORDINATES The last position output (seq=4000) takes 0.020 seconds, 1491.301 MB of memory in use WRITING VELOCITIES TO RESTART FILE AT STEP 4000 FINISHED WRITING RESTART VELOCITIES The last velocity output (seq=4000) takes 0.006 seconds, 1491.301 MB of memory in use LDB: ============= START OF LOAD BALANCING ============== 461.616 LDB: ============== END OF LOAD BALANCING =============== 461.617 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 461.618 LDB: ============= START OF LOAD BALANCING ============== 473.542 LDB: Largest compute 137 load 0.637508 is 7.3% of average load 8.687999 LDB: Average compute 0.077847 is 0.9% of average load 8.687999 LDB: TIME 473.562 LOAD: AVG 8.688 MAX 10.315 PROXIES: TOTAL 340 MAXPE 19 MAXPATCH 5 None MEM: 1491.3 MB LDB: TIME 473.563 LOAD: AVG 8.688 MAX 10.315 PROXIES: TOTAL 340 MAXPE 19 MAXPATCH 5 RefineTorusLB MEM: 1491.3 MB LDB: TIME 473.572 LOAD: AVG 8.688 MAX 8.86569 PROXIES: TOTAL 350 MAXPE 21 MAXPATCH 5 RefineTorusLB MEM: 1491.3 MB LDB: ============== END OF LOAD BALANCING =============== 473.593 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 473.837