Charm++: scheduler running in netpoll mode. Info: NAMD 2.6 for Linux-i686-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-tcp-iccstatic Info: Built Wed Aug 30 13:00:33 CDT 2006 by jim on verdun.ks.uiuc.edu Info: 1 NAMD 2.6 Linux-i686-TCP 2 node2 root Info: Running on 2 processors. Info: 7372 kB of memory in use. Info: Memory usage based on mallinfo Info: Configuration file is eq_test_cluster.txt TCL: Suspending until startup complete. Warning: The following variables were set in the Warning: configuation file but were not needed Warning: fixedAtomsForces Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 Info: NUMBER OF STEPS 0 Info: STEPS PER CYCLE 10 Info: LOAD BALANCE STRATEGY Other Info: LDB PERIOD 2000 steps Info: FIRST LDB TIMESTEP 50 Info: LDB BACKGROUND SCALING 1 Info: HOM 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: INITIAL TEMPERATURE 300 Info: CENTER OF MASS MOVING INITIALLY? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 SCALE FACTOR 1 Info: DCD FILENAME eq_test_cluster.dcd Info: DCD FREQUENCY 500 Info: DCD FIRST STEP 500 Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME eq_test_cluster Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME eq_test_cluster.restart Info: RESTART FREQUENCY 500 Info: BINARY RESTART FILES WILL BE USED 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: ENERGY OUTPUT STEPS 100 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 1000 Info: PRESSURE OUTPUT STEPS 100 Info: SPHERICAL BOUNDARY CONDITIONS ACTIVE Info: RADIUS #1 35 Info: FORCE CONSTANT #1 10 Info: EXPONENT #1 2 Info: SPHERE BOUNDARY CENTER(29.4094, 20.2894, 3.20805) 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 : ALL Info: ERROR TOLERANCE : 1e-08 Info: MAX ITERATIONS : 100 Info: RIGID WATER USING SETTLE ALGORITHM Info: RANDOM NUMBER SEED 1173208107 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB min_test_cluster.pdb Info: STRUCTURE FILE test_cluster.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS par_all27_prot_na_urea.inp Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: SUMMARY OF PARAMETERS: Info: 250 BONDS Info: 624 ANGLES Info: 1050 DIHEDRAL Info: 74 IMPROPER Info: 0 CROSSTERM Info: 130 VDW Info: 0 VDW_PAIRS Info: **************************** Info: STRUCTURE SUMMARY: Info: 18197 ATOMS Info: 13038 BONDS Info: 9683 ANGLES Info: 5310 DIHEDRALS Info: 1212 IMPROPERS Info: 0 CROSSTERMS Info: 0 EXCLUSIONS Info: 16311 RIGID BONDS Info: 38280 DEGREES OF FREEDOM Info: 6704 HYDROGEN GROUPS Info: TOTAL MASS = 114729 amu Info: TOTAL CHARGE = 1.64192e-05 e Info: ***************************** Info: Entering startup phase 0 with 7372 kB of memory in use. Info: Entering startup phase 1 with 7372 kB of memory in use. Info: Entering startup phase 2 with 9340 kB of memory in use. Info: Entering startup phase 3 with 9436 kB of memory in use. Info: PATCH GRID IS 4 BY 4 BY 4 Info: REMOVING COM VELOCITY -0.0107156 0.0418675 -0.0105978 Info: LARGEST PATCH (24) HAS 484 ATOMS Info: CREATING 1305 COMPUTE OBJECTS Info: Entering startup phase 4 with 12372 kB of memory in use. Info: Entering startup phase 5 with 12372 kB of memory in use. Info: Entering startup phase 6 with 12372 kB of memory in use. Measuring processor speeds... Done. Info: Entering startup phase 7 with 12372 kB of memory in use. Info: CREATING 1305 COMPUTE OBJECTS Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 4.44089e-16 AT 0.121031 Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.04308e-13 AT 11.9138 Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 1.69407e-21 AT 11.9974 Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.09878e-16 AT 11.9974 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 12740 kB of memory in use. Info: Finished startup with 16324 kB of memory in use. REINITIALIZING VELOCITIES AT STEP 0 TO 300 KELVIN. TCL: Running for 500000 steps PRESSURE: 0 0 0 0 0 0 0 0 0 0 GPRESSURE: 0 0 0 0 0 0 0 0 0 0 ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG ENERGY: 0 432.9413 1951.4299 908.8550 199.5182 -110215.1491 6278.5195 6229.1320 0.0000 11314.3989 -82900.3543 297.4746 -82882.5863 -82882.5863 297.4746 Info: Initial time: 2 CPUs 0.265826 s/step 1.53834 days/ns 25720 kB memory LDB: LOAD: AVG 11.3763 MAX 12.9585 MSGS: TOTAL 16 MAXC 16 MAXP 1 None Info: Adjusted background load on 1 nodes. LDB: LOAD: AVG 11.4018 MAX 13.6821 MSGS: TOTAL 48 MAXC 32 MAXP 1 Alg7 LDB: LOAD: AVG 11.4018 MAX 11.956 MSGS: TOTAL 48 MAXC 32 MAXP 1 Alg7 PRESSURE: 100 0 0 0 0 0 0 0 0 0 GPRESSURE: 100 0 0 0 0 0 0 0 0 0 PRESSAVG: 100 0 0 0 0 0 0 0 0 0 GPRESSAVG: 100 0 0 0 0 0 0 0 0 0 Info: Initial time: 2 CPUs 0.260022 s/step 1.50476 days/ns 30384 kB memory ENERGY: 100 703.2454 2116.0350 970.9193 227.1193 -106910.2473 5676.6493 96.5510 0.0000 11833.7705 -85285.9575 311.1298 -85239.1850 -85245.8786 305.7715