Charm++: standalone mode (not using charmrun)
Charm++> cpu topology info is being gathered. 
Charm++> 1 unique compute nodes detected. 
Info: NAMD 2.7b1 for Linux-x86_64
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 60100 for net-linux-x86_64-iccstatic
Info: Built Mon May 4 16:23:25 PDT 2009 by rok on morgan.ucsd.edu
Info: 1 NAMD  2.7b1  Linux-x86_64  1    morgan.ucsd.edu  rok
Info: Running on 1 processors.
Info: Charm++/Converse parallel runtime startup completed at 0.00307798 s
Info: 1.51997 MB of memory in use based on CmiMemoryUsage
Info: Configuration file is apbs-visualization.conf
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               1
Info: NUMBER OF STEPS        0
Info: STEPS PER CYCLE        20
Info: LOAD BALANCE STRATEGY  New Load Balancers -- ASB
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: MAX SELF PARTITIONS    20
Info: MAX PAIR PARTITIONS    8
Info: SELF PARTITION ATOMS   154
Info: SELF2 PARTITION ATOMS   154
Info: PAIR PARTITION ATOMS   318
Info: PAIR2 PARTITION ATOMS  637
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       0.833333
Info: DCD FILENAME           output.dcd
Info: DCD FREQUENCY          500
Info: DCD FIRST STEP         500
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME        output
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME       output.restart
Info: RESTART FREQUENCY      500
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON           9
Info: SWITCHING OFF          10
Info: PAIRLIST DISTANCE      11
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        13.5
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    100
Info: APBS SOLVATION FORCES ACTIVE
Info:     APBS PQR FILE: dipeptide.pqr
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   300
Info: LANGEVIN DAMPING COEFFICIENT IS 2 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: RANDOM NUMBER SEED     1241479450
Info: USE HYDROGEN BONDS?    NO
Info: Using AMBER format force field!
Info: AMBER PARM FILE        dipeptide.top
Info: AMBER COORDINATE FILE  dipeptide.crd
Info: Exclusions will be read from PARM file!
Info: SCNB (VDW SCALING)     2
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Reading parm file (dipeptide.top) ...
PARM file in AMBER 7 format
Info: SUMMARY OF PARAMETERS:
Info: 8 BONDS
Info: 14 ANGLES
Info: 20 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 0 VDW
Info: 28 VDW_PAIRS
Info: TIME FOR READING PDB FILE: 0
Info: 
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 20 ATOMS
Info: 19 BONDS
Info: 32 ANGLES
Info: 53 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 91 EXCLUSIONS
Info: 60 DEGREES OF FREEDOM
Info: 10 HYDROGEN GROUPS
Info: TOTAL MASS = 142.16 amu
Info: TOTAL CHARGE = 1.11759e-08 e
Info: *****************************
Info: 
Info: Entering startup at 0.022475 s, 1.75603 MB of memory in use
Info: Startup phase 0 took 2.31266e-05 s, 1.75612 MB of memory in use
Info: Startup phase 1 took 0.000101805 s, 1.76848 MB of memory in use
Info: Startup phase 2 took 2.59876e-05 s, 1.77174 MB of memory in use
Info: PATCH GRID IS 1 BY 1 BY 1
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY -2.16119 3.76538 0.300987
Info: LARGEST PATCH (0) HAS 20 ATOMS
Info: CREATING 12 COMPUTE OBJECTS
Info: Startup phase 3 took 0.000138998 s, 1.80525 MB of memory in use
Info: Startup phase 4 took 1.40667e-05 s, 1.80513 MB of memory in use
Info: Startup phase 5 took 1.69277e-05 s, 1.80501 MB of memory in use
LDB: Measuring processor speeds ... Done.
Info: Startup phase 6 took 4.31538e-05 s, 1.80641 MB of memory in use
Info: CREATING 12 COMPUTE OBJECTS
Info: useSync: 1 useProxySync: 0
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 705 POINTS
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 7.88861e-31 AT 9.99687
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 1.10587e-16 AT 9.99687
APBS: reading PQR file dipeptide.pqr
APBS: total charge: 0.4061
Info: Startup phase 7 took 0.00160599 s, 2.1953 MB of memory in use
Info: Startup phase 8 took 5.00679e-05 s, 2.44762 MB of memory in use
Info: Finished startup at 0.0244951 s, 2.44762 MB of memory in use

TCL: Minimizing for 0 steps
  Writing potential to iapbs-pot.dx
APBS ENERGIES: ELEC: 367.934 NONPOLAR: 9.09946
ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP               ELECT            VDW       BOUNDARY           MISC        KINETIC               TOTAL           TEMP      POTENTIAL         TOTAL3        TEMPAVG

ENERGY:       0         0.0006         0.6006         3.6494         0.0000             18.5634         7.3412         0.0000       377.0339         0.0000            407.1891         0.0000       407.1891       407.1891         0.0000

WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 0
WRITING COORDINATES TO OUTPUT FILE AT STEP 0
COORDINATE DCD FILE WAS NOT CREATED
WRITING VELOCITIES TO OUTPUT FILE AT STEP 0
====================================================

WallClock: 0.222357  CPUTime: 0.204013  Memory: 2.345078 MB
Program finished.
