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