Charm++: scheduler running in netpoll mode. Info: NAMD 2.6 for Linux-i686-Clustermatic4-TCP Info: Info: Please visit http://www.ks.uiuc.edu/Research/namd/ Info: and send feedback or bug reports to namd@ks.uiuc.edu 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 50900 for net-linux-clustermatic-tcp-iccstatic Info: Built Wed Aug 30 12:58:29 CDT 2006 by jim on portia.ks.uiuc.edu Info: 1 NAMD 2.6 Linux-i686-Clustermatic4-TCP 48 portia.ks.uiuc.edu jcomer Info: Running on 48 processors. Info: 7392 kB of memory in use. Info: Memory usage based on mallinfo Info: Configuration file is eq3.namd TCL: Suspending until startup complete. Info: EXTENDED SYSTEM FILE eq2.restart.xsc Info: SIMULATION PARAMETERS: Info: TIMESTEP 1 Info: NUMBER OF STEPS 100000 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 33.2575 19.1751 0 Info: PERIODIC CELL BASIS 2 0 38.3502 0 Info: PERIODIC CELL BASIS 3 0 0 50.5552 Info: PERIODIC CELL CENTER 0 0 0 Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT. Info: WRAPPING TO IMAGE NEAREST TO PERIODIC CELL CENTER. Info: LOAD BALANCE STRATEGY Other Info: LDB PERIOD 4000 steps Info: FIRST LDB TIMESTEP 100 Info: LDB BACKGROUND SCALING 1 Info: HOM BACKGROUND SCALING 1 Info: PME BACKGROUND SCALING 1 Info: MAX SELF PARTITIONS 50 Info: MAX PAIR PARTITIONS 20 Info: SELF PARTITION ATOMS 125 Info: PAIR PARTITION ATOMS 200 Info: PAIR2 PARTITION ATOMS 400 Info: MIN ATOMS PER PATCH 100 Info: VELOCITY FILE eq2.restart.vel Info: CENTER OF MASS MOVING INITIALLY? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 SCALE FACTOR 1 Info: DCD FILENAME eq3.dcd Info: DCD FREQUENCY 1000 Info: DCD FIRST STEP 1000 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME eq3.xst Info: XST FREQUENCY 1000 Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME eq3 Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME eq3.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 3 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 19.5 Info: ENERGY OUTPUT STEPS 1000 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 1000 Info: HARMONIC CONSTRAINTS ACTIVE Info: HARMONIC CONS EXP 2 Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 295 Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE Info: TARGET PRESSURE IS 1.01325 BAR Info: OSCILLATION PERIOD IS 200 FS Info: DECAY TIME IS 200 FS Info: PISTON TEMPERATURE IS 295 K Info: PRESSURE CONTROL IS ATOM-BASED Info: INITIAL STRAIN RATE IS 0.000302079 8.73502e-05 0.000118309 Info: CELL FLUCTUATION IS ANISOTROPIC 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 48 48 64 Info: PME MAXIMUM GRID SPACING 1.5 Info: Attempting to read FFTW data from FFTW_NAMD_2.6_Linux-i686-Clustermatic4-TCP.txt Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done. Info: Writing FFTW data to FFTW_NAMD_2.6_Linux-i686-Clustermatic4-TCP.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: NONBONDED FORCES EVALUATED EVERY 2 STEPS Info: RANDOM NUMBER SEED 1163403380 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB pore_all.pdb Info: STRUCTURE FILE pore_all.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS cornell.prm Info: PARAMETERS par_silicon_ions_NEW5.inp Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: BINARY COORDINATES eq2.restart.coor Info: SUMMARY OF PARAMETERS: Info: 96 BONDS Info: 229 ANGLES Info: 81 DIHEDRAL Info: 31 IMPROPER Info: 0 CROSSTERM Info: 62 VDW Info: 0 VDW_PAIRS Info: **************************** Info: STRUCTURE SUMMARY: Info: 5545 ATOMS Info: 5274 BONDS Info: 7833 ANGLES Info: 0 DIHEDRALS Info: 0 IMPROPERS Info: 0 CROSSTERMS Info: 0 EXCLUSIONS Info: 1758 CONSTRAINTS Info: 16635 DEGREES OF FREEDOM Info: 3087 HYDROGEN GROUPS Info: TOTAL MASS = 60995.4 amu Info: TOTAL CHARGE = -0.00015521 e Info: ***************************** Info: Entering startup phase 0 with 7392 kB of memory in use. Info: Entering startup phase 1 with 7392 kB of memory in use. Info: Entering startup phase 2 with 7392 kB of memory in use. Info: Entering startup phase 3 with 7392 kB of memory in use. Info: PATCH GRID IS 1 (PERIODIC) BY 1 (PERIODIC) BY 2 (PERIODIC) Info: REMOVING COM VELOCITY 0.00068377 0.042765 0.0378741 Info: LARGEST PATCH (0) HAS 2775 ATOMS Info: CREATING 644 COMPUTE OBJECTS Info: Entering startup phase 4 with 7392 kB of memory in use. Info: PME using 48 and 48 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: Optimizing 4 FFT steps. 1... 2... 3... 4... Done. Info: Entering startup phase 5 with 7392 kB of memory in use. Info: Entering startup phase 6 with 7392 kB of memory in use. Measuring processor speeds... Done. Info: Entering startup phase 7 with 7392 kB of memory in use. Info: CREATING 644 COMPUTE OBJECTS Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 4.3715e-16 AT 0.03125 Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.00929e-16 AT 0.231756 Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 3.70577e-22 AT 11.9974 Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 2.80873e-16 AT 11.9138 Info: ABSOLUTE IMPRECISION IN SCOR TABLE ENERGY: 2.91168e-22 AT 11.9974 Info: RELATIVE IMPRECISION IN SCOR TABLE ENERGY: 6.16001e-17 AT 11.9974 Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 1.98523e-22 AT 11.9974 Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 8.0593e-16 AT 11.9138 Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.97215e-31 AT 11.8295 Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.72641e-14 AT 11.9138 Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 8.32002e-32 AT 11.9974 Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 1.83939e-15 AT 11.9138 Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 8.80495e-26 AT 11.9974 Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-15 AT 11.9138 Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 5.16988e-26 AT 11.9138 Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 7.96546e-16 AT 11.9138 Info: Entering startup phase 8 with 7392 kB of memory in use. Info: Finished startup with 7392 kB of memory in use. ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY: 0 1938.8644 556.7655 0.0000 0.0000 -230697.1751 3530.4215 976.4058 0.0000 5202.9823 -218491.7356 314.7893 -218425.8890 -218425.8890 314.7893 -1072.3089 -2817.1108 64479.7085 -1072.3089 -2817.1108 OPENING EXTENDED SYSTEM TRAJECTORY FILE Info: Initial time: 48 CPUs 0.129715 s/step 1.50134 days/ns 7392 kB memory LDB: LOAD: AVG 0.769261 MAX 10.1084 MSGS: TOTAL 50 MAXC 2 MAXP 25 None Info: Adjusted background load on 40 nodes. Info: 630 of 630 computes have background load > 0.46323 Info: 630 of 630 computes have background load > 0.555876 Info: 630 of 630 computes have background load > 0.648522 Info: 630 of 630 computes have background load > 0.741168 Info: 630 of 630 computes have background load > 0.833814 Info: 630 of 630 computes have background load > 0.92646 Info: 630 of 630 computes have background load > 1.01911 Info: 630 of 630 computes have background load > 1.11175 Info: 630 of 630 computes have background load > 1.2044 Info: 630 of 630 computes have background load > 1.29704 Info: 630 of 630 computes have background load > 1.38969 Info: 630 of 630 computes have background load > 1.48234 Info: 630 of 630 computes have background load > 1.57498 Info: 630 of 630 computes have background load > 1.66763 Info: 630 of 630 computes have background load > 1.76027 Info: 630 of 630 computes have background load > 1.85292 Info: 630 of 630 computes have background load > 1.94557 Info: 630 of 630 computes have background load > 2.03821 Info: 630 of 630 computes have background load > 2.13086 Info: 630 of 630 computes have background load > 2.2235 Info: 630 of 630 computes have background load > 2.31615 Info: 630 of 630 computes have background load > 2.4088 Info: 630 of 630 computes have background load > 2.50144 Info: 630 of 630 computes have background load > 2.59409 Info: 630 of 630 computes have background load > 2.68673 Info: 630 of 630 computes have background load > 2.77938 Info: 630 of 630 computes have background load > 2.87203 Info: 630 of 630 computes have background load > 2.96467 Info: 495 of 630 computes have background load > 3.05732 Info: 495 of 630 computes have background load > 3.14996 Info: 495 of 630 computes have background load > 3.24261 Info: 495 of 630 computes have background load > 3.33526 Info: 495 of 630 computes have background load > 3.4279 Info: 495 of 630 computes have background load > 3.52055 Info: 495 of 630 computes have background load > 3.61319 Info: 495 of 630 computes have background load > 3.70584 Info: 495 of 630 computes have background load > 3.79849 Info: 495 of 630 computes have background load > 3.89113 Info: 495 of 630 computes have background load > 3.98378 Info: 495 of 630 computes have background load > 4.07642 Info: 495 of 630 computes have background load > 4.16907 Info: 495 of 630 computes have background load > 4.26172 LDB: LOAD: AVG 0.92646 MAX 4.2979 MSGS: TOTAL 58 MAXC 2 MAXP 31 Alg7 Warning: 3 processors are overloaded due to high background load. LDB: LOAD: AVG 0.92646 MAX 4.2979 MSGS: TOTAL 58 MAXC 2 MAXP 31 Alg7 Info: Initial time: 48 CPUs 0.126879 s/step 1.46851 days/ns 7392 kB memory LDB: LOAD: AVG 1.16717 MAX 8.91915 MSGS: TOTAL 58 MAXC 2 MAXP 31 None Warning: 2 processors are overloaded due to high background load. LDB: LOAD: AVG 1.16717 MAX 8.91915 MSGS: TOTAL 58 MAXC 2 MAXP 31 Refine Info: Initial time: 48 CPUs 0.175586 s/step 2.03225 days/ns 7392 kB memory LDB: LOAD: AVG 1.09336 MAX 7.22658 MSGS: TOTAL 58 MAXC 2 MAXP 31 None Warning: 2 processors are overloaded due to high background load. LDB: LOAD: AVG 1.09336 MAX 7.22658 MSGS: TOTAL 58 MAXC 2 MAXP 31 Refine Info: Benchmark time: 48 CPUs 0.176125 s/step 2.03848 days/ns 7428 kB memory Info: Benchmark time: 48 CPUs 0.18453 s/step 2.13576 days/ns 7428 kB memory Info: Benchmark time: 48 CPUs 0.193397 s/step 2.23839 days/ns 7428 kB memory TIMING: 1000 CPU: 6.35, 0.00634/step Wall: 177.379, 0.176468/step, 4.85286 hours remaining, 7428 kB of memory in use. ENERGY: 1000 1928.5472 524.3485 0.0000 0.0000 -231939.5097 4018.0598 1012.5847 0.0000 5019.4172 -219436.5523 303.6833 -219370.4924 -219373.2069 309.9224 2472.0652 257.9799 61803.3440 1.2204 2.4038 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1000 OPENING COORDINATE DCD FILE WRITING COORDINATES TO DCD FILE AT STEP 1000 WRITING COORDINATES TO RESTART FILE AT STEP 1000 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 1000 FINISHED WRITING RESTART VELOCITIES TIMING: 2000 CPU: 13.71, 0.00736/step Wall: 373.127, 0.195748/step, 5.3287 hours remaining, 7968 kB of memory in use. ENERGY: 2000 1930.5273 586.0746 0.0000 0.0000 -232255.4617 3969.4184 1023.9736 0.0000 4765.7987 -219979.6691 288.3389 -219914.2040 -219911.0343 301.3830 105.3556 -1791.3539 60164.3618 -28.6856 -28.9253 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 2000 WRITING COORDINATES TO DCD FILE AT STEP 2000 WRITING COORDINATES TO RESTART FILE AT STEP 2000 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 2000 FINISHED WRITING RESTART VELOCITIES TIMING: 3000 CPU: 21.26, 0.00755/step Wall: 572.525, 0.199398/step, 5.37267 hours remaining, 7968 kB of memory in use. ENERGY: 3000 1952.3261 530.4677 0.0000 0.0000 -232757.7090 4170.3544 1050.4844 0.0000 4913.5963 -220140.4800 297.2809 -220074.4320 -220074.5007 295.3726 2737.4489 647.4177 59014.2367 -19.5857 -20.0743 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 3000 WRITING COORDINATES TO DCD FILE AT STEP 3000 WRITING COORDINATES TO RESTART FILE AT STEP 3000 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 3000 FINISHED WRITING RESTART VELOCITIES TIMING: 4000 CPU: 30.3, 0.00904/step Wall: 774.89, 0.202365/step, 5.3964 hours remaining, 7972 kB of memory in use. ENERGY: 4000 1899.1503 496.7915 0.0000 0.0000 -232868.3023 4232.8597 1033.4497 0.0000 4907.4203 -220298.6308 296.9073 -220229.1950 -220240.9614 297.0979 3236.1401 313.9189 58147.8694 17.3012 16.6874 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 4000 WRITING COORDINATES TO DCD FILE AT STEP 4000 WRITING COORDINATES TO RESTART FILE AT STEP 4000 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 4000 FINISHED WRITING RESTART VELOCITIES LDB: LOAD: AVG 1.271 MAX 10.8236 MSGS: TOTAL 58 MAXC 2 MAXP 31 None Warning: 2 processors are overloaded due to high background load. LDB: LOAD: AVG 1.271 MAX 10.8236 MSGS: TOTAL 58 MAXC 2 MAXP 31 Refine TIMING: 5000 CPU: 37.61, 0.00731/step Wall: 974.712, 0.199822/step, 5.27308 hours remaining, 7972 kB of memory in use. ENERGY: 5000 1933.0679 578.0867 0.0000 0.0000 -232571.7543 3929.9656 982.0729 0.0000 4992.2295 -220156.3318 302.0384 -220090.8689 -220086.5455 297.3319 459.9446 -1843.3476 57829.5908 -13.2733 -13.3245 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 5000 WRITING COORDINATES TO DCD FILE AT STEP 5000 WRITING COORDINATES TO RESTART FILE AT STEP 5000 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 5000 FINISHED WRITING RESTART VELOCITIES TIMING: 6000 CPU: 46.6, 0.00899/step Wall: 1170.83, 0.196122/step, 5.12097 hours remaining, 8024 kB of memory in use. ENERGY: 6000 1942.9447 564.8991 0.0000 0.0000 -232774.2537 4033.9708 955.1734 0.0000 4885.3416 -220391.9240 295.5715 -220325.5233 -220322.7156 297.1986 1457.1049 -1206.4711 57643.3089 -26.7349 -26.2337 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 6000 WRITING COORDINATES TO DCD FILE AT STEP 6000 WRITING COORDINATES TO RESTART FILE AT STEP 6000 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 6000 FINISHED WRITING RESTART VELOCITIES TIMING: 7000 CPU: 53.83, 0.00723/step Wall: 1367.46, 0.196626/step, 5.07949 hours remaining, 8024 kB of memory in use. ENERGY: 7000 1977.0985 547.3253 0.0000 0.0000 -232889.5941 4065.6765 1036.0924 0.0000 4897.7638 -220365.6375 296.3230 -220300.5927 -220292.8269 297.0819 2420.7689 740.3431 57288.1944 17.7961 17.6768 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 7000 WRITING COORDINATES TO DCD FILE AT STEP 7000 WRITING COORDINATES TO RESTART FILE AT STEP 7000 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 7000 FINISHED WRITING RESTART VELOCITIES WRITING COORDINATES TO DCD FILE AT STEP 8000 WRITING COORDINATES TO RESTART FILE AT STEP 8000 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 8000 FINISHED WRITING RESTART VELOCITIES TIMING: 8000 CPU: 60.55, 0.00672/step Wall: 1564.4, 0.19694/step, 5.03291 hours remaining, 8056 kB of memory in use. ENERGY: 8000 1919.9270 555.3877 0.0000 0.0000 -233017.0844 4205.6103 1018.7363 0.0000 4853.3129 -220464.1102 293.6337 -220398.2904 -220393.6091 296.7856 3118.6187 680.2101 56805.4923 31.5520 32.4900 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 8000 LDB: LOAD: AVG 1.26339 MAX 11.2797 MSGS: TOTAL 58 MAXC 2 MAXP 31 None Warning: 2 processors are overloaded due to high background load. LDB: LOAD: AVG 1.26339 MAX 11.2797 MSGS: TOTAL 58 MAXC 2 MAXP 31 Refine TIMING: 9000 CPU: 67.59, 0.00704/step Wall: 1766.08, 0.201679/step, 5.09801 hours remaining, 8056 kB of memory in use. ENERGY: 9000 1930.2879 593.7770 0.0000 0.0000 -232616.1162 3857.9458 994.5127 0.0000 4831.6348 -220407.9580 292.3221 -220341.8265 -220342.2803 295.5192 -912.8584 -2949.8263 57204.4024 -26.7382 -27.2353 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 9000 WRITING COORDINATES TO DCD FILE AT STEP 9000 WRITING COORDINATES TO RESTART FILE AT STEP 9000 FINISHED WRITING RESTART COORDINATES WRITING VELOCITIES TO RESTART FILE AT STEP 9000 FINISHED WRITING RESTART VELOCITIES