Charm++: standalone mode (not using charmrun)
Info: NAMD 2.6 for Linux-amd64
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-amd64-iccstatic
Info: Built Wed Aug 30 12:54:51 CDT 2006 by jim on belfast.ks.uiuc.edu
Info: 1 NAMD  2.6  Linux-amd64  1    tbgl-work3.physics.uiuc.edu  david
Info: Running on 1 processors.
Info: 7476 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Configuration file is rot-b-short.namd
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE   ../common/rot-eq-2.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               1
Info: NUMBER OF STEPS        100
Info: STEPS PER CYCLE        20
Info: PERIODIC CELL BASIS 1  50 0 0
Info: PERIODIC CELL BASIS 2  0 50 0
Info: PERIODIC CELL BASIS 3  0 0 50
Info: PERIODIC CELL CENTER   0 0 0
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          ../common/rot-eq-2.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           rot-b-short.dcd
Info: DCD FREQUENCY          100
Info: DCD FIRST STEP         100
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME           rot-b-short.xst
Info: XST FREQUENCY          100
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME        rot-b-short
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME       rot-b-short.restart
Info: RESTART FREQUENCY      100
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                 5
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        21.5
Info: ENERGY OUTPUT STEPS    100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    100
Info: TCL GLOBAL FORCES ACTIVE
Info: TCL GLOBAL FORCES SCRIPT   rot-b.tcl
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   288
Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
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 48
Info: PME MAXIMUM GRID SPACING    1.5
Info: Attempting to read FFTW data from FFTW_NAMD_2.6_Linux-amd64.txt
Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
Info: Writing FFTW data to FFTW_NAMD_2.6_Linux-amd64.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     1173743368
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         ../common/ubiquitin_solvate.pdb
Info: STRUCTURE FILE         ../common/ubiquitin_solvate.psf
Info: PARAMETER file: CHARMM format! 
Info: PARAMETERS             ../common/par_all27_na.inp
Info: PARAMETERS             ../common/par_all27_prot_lipid.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES     ../common/rot-eq-2.coor

Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2
PREVIOUS VALUES  k=130  theta0=107 k_ub=0 r_ub=0
   USING VALUES  k=130  theta0=107.5 k_ub=0 r_ub=0
Warning: DUPLICATE vdW ENTRY FOR DUM
PREVIOUS VALUES  sigma=1.7818 epsilon=0 sigma14=1.7818 epsilon14=0
   USING VALUES  sigma=0 epsilon=0 sigma14=0 epsilon14=0
Info: SUMMARY OF PARAMETERS:
Info: 298 BONDS
Info: 729 ANGLES
Info: 1145 DIHEDRAL
Info: 84 IMPROPER
Info: 0 CROSSTERM
Info: 168 VDW
Info: 0 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 11317 ATOMS
Info: 7961 BONDS
Info: 5619 ANGLES
Info: 3293 DIHEDRALS
Info: 204 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 33951 DEGREES OF FREEDOM
Info: 3964 HYDROGEN GROUPS
Info: TOTAL MASS = 69132.6 amu
Info: TOTAL CHARGE = 1.0021e-06 e
Info: *****************************
Info: Entering startup phase 0 with 7476 kB of memory in use.
Info: Entering startup phase 1 with 7476 kB of memory in use.
Info: Entering startup phase 2 with 8096 kB of memory in use.
Info: Entering startup phase 3 with 8096 kB of memory in use.
Info: PATCH GRID IS 2 (PERIODIC) BY 2 (PERIODIC) BY 2 (PERIODIC)
Info: REMOVING COM VELOCITY -0.0715685 0.0080218 -0.0901703
Info: LARGEST PATCH (7) HAS 1504 ATOMS
Info: CREATING 1927 COMPUTE OBJECTS
Info: Entering startup phase 4 with 10260 kB of memory in use.
Info: PME using 1 and 1 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 0
Info: PME TRANS LOCATIONS: 0
Info: Optimizing 4 FFT steps.  1... 2... 3... 4...   Done.
Info: Entering startup phase 5 with 10260 kB of memory in use.
Info: Entering startup phase 6 with 10260 kB of memory in use.
Measuring processor speeds... Done.
Info: Entering startup phase 7 with 10260 kB of memory in use.
Info: CREATING 1927 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
TCL: Linear acceleration applied: (10 0 0) Ang*ps^-2
TCL: Angular acceleration applied: (0 0 1) Rad*ps^-2
Info: Entering startup phase 8 with 14412 kB of memory in use.
Info: Finished startup with 15104 kB of memory in use.
TCL: Center of mass = -0.192638367627 0.243249895589 -0.11600245128
TCL: atom 1: phi = -0.593067026911
ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP               ELECT            VDW       BOUNDARY           MISC        KINETIC               TOTAL           TEMP         TOTAL2         TOTAL3        TEMPAVG            PRESSURE      GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG

ENERGY:       0      3320.9226      2485.4973       369.2281        41.8925         -45062.6110      4213.7486         0.0000         0.0000      9511.9860         -25119.3360       281.9740    -24978.2453    -24978.2453       281.9740            448.5697     -1937.0307    125000.0000       448.5697     -1937.0307

OPENING EXTENDED SYSTEM TRAJECTORY FILE
TCL: Center of mass = -0.192480341339 0.243106254141 -0.115983413026
TCL: atom 1: phi = -0.592587509643
TCL: Center of mass = -0.19231095076 0.242941142161 -0.115936392295
TCL: atom 1: phi = -0.591991992254
TCL: Center of mass = -0.192154374895 0.242764957024 -0.115891260548
TCL: atom 1: phi = -0.591482057245
TCL: Center of mass = -0.192004293085 0.242550682778 -0.115799001149
TCL: atom 1: phi = -0.590904011958
TCL: Center of mass = -0.191895538078 0.242343333529 -0.115730329913
TCL: atom 1: phi = -0.590465228929
TCL: Center of mass = -0.191786716262 0.24212231049 -0.115645576873
TCL: atom 1: phi = -0.590006111305
TCL: Center of mass = -0.191686558074 0.241921688576 -0.115551574669
TCL: atom 1: phi = -0.589596614952
TCL: Center of mass = -0.191571163032 0.241742416194 -0.115449592089
TCL: atom 1: phi = -0.589084487482
TCL: Center of mass = -0.191435225931 0.24161148791 -0.115361262437
TCL: atom 1: phi = -0.588629632946
TCL: Center of mass = -0.191242303985 0.241474886254 -0.115261351093
TCL: atom 1: phi = -0.588206368699
TCL: Center of mass = -0.191011577737 0.241365801657 -0.115174677206
TCL: atom 1: phi = -0.5880446656
TCL: Center of mass = -0.190726307969 0.241244689894 -0.115070474679
TCL: atom 1: phi = -0.588010878302
TCL: Center of mass = -0.190390666617 0.241128031128 -0.114959375047
TCL: atom 1: phi = -0.588333469615
TCL: Center of mass = -0.190010323815 0.240966517675 -0.114814648389
TCL: atom 1: phi = -0.588861870777
TCL: Center of mass = -0.189595883394 0.240808437627 -0.114649529859
TCL: atom 1: phi = -0.589660383188
TCL: Center of mass = -0.189170657562 0.240631913566 -0.114464283468
TCL: atom 1: phi = -0.59061448831
TCL: Center of mass = -0.188740075792 0.240446854715 -0.114283541454
TCL: atom 1: phi = -0.591746881402
TCL: Center of mass = -0.188314918661 0.240264774031 -0.114108690363
TCL: atom 1: phi = -0.592772304629
TCL: Center of mass = -0.187895377439 0.240120939955 -0.113934295884
TCL: atom 1: phi = -0.593788807172
TCL: Center of mass = -0.187465718466 0.240006511299 -0.113772089209
TCL: atom 1: phi = -0.594616870495
TCL: Center of mass = -0.187071222281 0.239939240775 -0.113645014974
TCL: atom 1: phi = -0.59541217275
TCL: Center of mass = -0.186685527598 0.239866691258 -0.113533059094
TCL: atom 1: phi = -0.595972300997
TCL: Center of mass = -0.186360999604 0.239809386989 -0.113445883748
TCL: atom 1: phi = -0.596537114612
TCL: Center of mass = -0.186077872598 0.239745955929 -0.113345016329
TCL: atom 1: phi = -0.597042394325
TCL: Center of mass = -0.185882725637 0.239668126933 -0.113245956478
TCL: atom 1: phi = -0.597566945386
TCL: Center of mass = -0.185731581506 0.239553464278 -0.1131504044
TCL: atom 1: phi = -0.597931209305
TCL: Center of mass = -0.185652473444 0.239437365009 -0.11308032686
TCL: atom 1: phi = -0.598235138941
TCL: Center of mass = -0.185625536213 0.239310820781 -0.113014373809
TCL: atom 1: phi = -0.598294471899
TCL: Center of mass = -0.185651898659 0.239210146561 -0.11295625707
TCL: atom 1: phi = -0.598322486569
TCL: Center of mass = -0.18567550102 0.2391149729 -0.112894305735
TCL: atom 1: phi = -0.598184782887
TCL: Center of mass = -0.185708236579 0.239047689828 -0.112831784791
TCL: atom 1: phi = -0.598100405135
TCL: Center of mass = -0.185713741974 0.238992724863 -0.112778608048
TCL: atom 1: phi = -0.59796003526
TCL: Center of mass = -0.185716395193 0.238962297435 -0.112724537482
TCL: atom 1: phi = -0.597982001294
TCL: Center of mass = -0.185699758681 0.238898755583 -0.112671151671
TCL: atom 1: phi = -0.598044963365
TCL: Center of mass = -0.185684761441 0.238811058621 -0.11261604802
TCL: atom 1: phi = -0.598326433532
TCL: Center of mass = -0.185649607115 0.238663901781 -0.112527617173
TCL: atom 1: phi = -0.598738955129
TCL: Center of mass = -0.185590956577 0.238482674608 -0.11245147572
TCL: atom 1: phi = -0.599410661142
TCL: Center of mass = -0.185474937716 0.238260594035 -0.112365952894
TCL: atom 1: phi = -0.600102531275
TCL: Center of mass = -0.185314107429 0.238032097851 -0.112272070596
TCL: atom 1: phi = -0.600872788844
TCL: Center of mass = -0.185091145778 0.237786403411 -0.11214780475
TCL: atom 1: phi = -0.601496985932
TCL: Center of mass = -0.184834285945 0.23754645218 -0.112014379243
TCL: atom 1: phi = -0.602049940543
TCL: Center of mass = -0.184553476036 0.23729595082 -0.111856411483
TCL: atom 1: phi = -0.602364198874
TCL: Center of mass = -0.184275961937 0.237055089986 -0.111681942897
TCL: atom 1: phi = -0.602591035087
TCL: Center of mass = -0.184001551726 0.236774995758 -0.111493902744
TCL: atom 1: phi = -0.6026219685
TCL: Center of mass = -0.183768176981 0.23648942543 -0.111289841891
TCL: atom 1: phi = -0.602665849786
TCL: Center of mass = -0.18352523799 0.236156088296 -0.111090349636
TCL: atom 1: phi = -0.602615398477
TCL: Center of mass = -0.183319305472 0.235789126905 -0.110888315618
TCL: atom 1: phi = -0.602628248426
TCL: Center of mass = -0.183116637555 0.235400442642 -0.110681752252
TCL: atom 1: phi = -0.602498676878
TCL: Center of mass = -0.182925165217 0.234992492191 -0.110495486956
TCL: atom 1: phi = -0.602392425042
TCL: Center of mass = -0.182717117516 0.234547046456 -0.110314063704
TCL: atom 1: phi = -0.602102230721
TCL: Center of mass = -0.182536834398 0.234101511226 -0.11014116162
TCL: atom 1: phi = -0.60184918276
TCL: Center of mass = -0.182369682112 0.233644383907 -0.109956917816
TCL: atom 1: phi = -0.601459418641
TCL: Center of mass = -0.182256809664 0.233194995762 -0.109774076889
TCL: atom 1: phi = -0.601138590659
TCL: Center of mass = -0.182185515178 0.232737902884 -0.109599657517
TCL: atom 1: phi = -0.600795680157
TCL: Center of mass = -0.182156802675 0.232306397898 -0.109434425273
TCL: atom 1: phi = -0.600637262055
TCL: Center of mass = -0.18212542021 0.231874007991 -0.109273169733
TCL: atom 1: phi = -0.600509012845
TCL: Center of mass = -0.182099339792 0.231449420955 -0.109139096791
TCL: atom 1: phi = -0.600637459903
TCL: Center of mass = -0.182049679108 0.231014480493 -0.108996305593
TCL: atom 1: phi = -0.600806335851
TCL: Center of mass = -0.181969182022 0.230593454925 -0.108845018944
TCL: atom 1: phi = -0.601179124388
TCL: Center of mass = -0.181846139929 0.230157011865 -0.108677762799
TCL: atom 1: phi = -0.601492550756
TCL: Center of mass = -0.181683943523 0.229733755308 -0.108537340493
TCL: atom 1: phi = -0.60181737411
TCL: Center of mass = -0.181504594926 0.229300070521 -0.108370707531
TCL: atom 1: phi = -0.601895626253
TCL: Center of mass = -0.181341701728 0.228909357703 -0.108196459733
TCL: atom 1: phi = -0.60189210335
TCL: Center of mass = -0.181182639932 0.228528646438 -0.107992925978
TCL: atom 1: phi = -0.601596495784
TCL: Center of mass = -0.181061780608 0.228186037647 -0.107798346697
TCL: atom 1: phi = -0.601261178012
TCL: Center of mass = -0.180931030885 0.227866271635 -0.10759562975
TCL: atom 1: phi = -0.600662487173
TCL: Center of mass = -0.180799274673 0.227557043672 -0.107409294945
TCL: atom 1: phi = -0.600040722686
TCL: Center of mass = -0.180657594956 0.227257807032 -0.107224714936
TCL: atom 1: phi = -0.599209549738
TCL: Center of mass = -0.18049410253 0.226992172478 -0.107044807812
TCL: atom 1: phi = -0.59841848829
TCL: Center of mass = -0.180311039429 0.226713107217 -0.106867838873
TCL: atom 1: phi = -0.597383374103
TCL: Center of mass = -0.18012797521 0.226458166551 -0.106704922639
TCL: atom 1: phi = -0.596334643841
TCL: Center of mass = -0.17995502619 0.226199631228 -0.106542265323
TCL: atom 1: phi = -0.595055175927
TCL: Center of mass = -0.179815597886 0.225958078788 -0.106364259818
TCL: atom 1: phi = -0.593850180318
TCL: Center of mass = -0.17972171754 0.225704747398 -0.106160020513
TCL: atom 1: phi = -0.592549870549
TCL: Center of mass = -0.179682913474 0.225462334241 -0.105980762803
TCL: atom 1: phi = -0.591506606558
TCL: Center of mass = -0.179682046585 0.225216270802 -0.10578581497
TCL: atom 1: phi = -0.590591037929
TCL: Center of mass = -0.179683341577 0.224986821717 -0.105611864508
TCL: atom 1: phi = -0.59003766981
TCL: Center of mass = -0.17963657526 0.224754764859 -0.105436400756
TCL: atom 1: phi = -0.589661638403
TCL: Center of mass = -0.179543377974 0.224532438209 -0.105303995418
TCL: atom 1: phi = -0.589722928494
TCL: Center of mass = -0.17942008179 0.224312094445 -0.105175552785
TCL: atom 1: phi = -0.58990500426
TCL: Center of mass = -0.179265425069 0.224102066489 -0.105088296009
TCL: atom 1: phi = -0.590404038916
TCL: Center of mass = -0.179095289901 0.223870815217 -0.105016425918
TCL: atom 1: phi = -0.590959637401
TCL: Center of mass = -0.178929671889 0.223635753162 -0.104974601909
TCL: atom 1: phi = -0.591673564178
TCL: Center of mass = -0.178770598438 0.223357190562 -0.104942505612
TCL: atom 1: phi = -0.592360959092
TCL: Center of mass = -0.178642259035 0.223064708008 -0.104932971659
TCL: atom 1: phi = -0.593169469197
TCL: Center of mass = -0.178522511316 0.222723989134 -0.104925739841
TCL: atom 1: phi = -0.593860304276
TCL: Center of mass = -0.178393382747 0.22237513626 -0.104959522142
TCL: atom 1: phi = -0.594591789422
TCL: Center of mass = -0.178215044348 0.222041144656 -0.105001221771
TCL: atom 1: phi = -0.595175976552
TCL: Center of mass = -0.17802438918 0.221709400291 -0.105076997055
TCL: atom 1: phi = -0.595817673486
TCL: Center of mass = -0.177789601187 0.221359660096 -0.105147127616
TCL: atom 1: phi = -0.596242909047
TCL: Center of mass = -0.177549298847 0.22100377679 -0.105244740798
TCL: atom 1: phi = -0.596578042203
TCL: Center of mass = -0.17731092151 0.220607082526 -0.105341948571
TCL: atom 1: phi = -0.596581255506
TCL: Center of mass = -0.17712724216 0.220178423806 -0.105435559146
TCL: atom 1: phi = -0.596513219258
TCL: Center of mass = -0.176995454169 0.219698254801 -0.105517719517
TCL: atom 1: phi = -0.596235270661
TCL: Center of mass = -0.176908289077 0.219191441854 -0.105593864605
TCL: atom 1: phi = -0.595989247675
TCL: Center of mass = -0.176840246629 0.21863780854 -0.105650485538
TCL: atom 1: phi = -0.595638376728
TCL: Center of mass = -0.176801824569 0.218081910703 -0.105717771615
TCL: atom 1: phi = -0.595501163318
TCL: Center of mass = -0.176733442476 0.217521553668 -0.105778122527
TCL: atom 1: phi = -0.59540631046
TCL: Center of mass = -0.176646870193 0.21698049839 -0.105844485357
TCL: atom 1: phi = -0.59556692793
TCL: Center of mass = -0.176538028098 0.216460692429 -0.105906221375
TCL: atom 1: phi = -0.595816648656
Info: Initial time: 1 CPUs 0.191622 s/step 2.21785 days/ns 52056 kB memory
TIMING: 100  CPU: 20.8828, 0.191121/step  Wall: 21.0467, 0.1917/step, 0 hours remaining, 52056 kB of memory in use.
ENERGY:     100      3331.0658      2404.0250       371.9085        36.7303         -44896.9487      4129.8614         0.0000         0.0000      9457.5670         -25165.7907       280.3608    -25023.7801    -25023.5714       280.8439            627.7212     -1851.2216    125000.0000     -1797.6945     -1797.1097

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 100
OPENING COORDINATE DCD FILE
WRITING COORDINATES TO DCD FILE AT STEP 100
WRITING COORDINATES TO RESTART FILE AT STEP 100
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 100
FINISHED WRITING RESTART VELOCITIES
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 100
CLOSING EXTENDED SYSTEM TRAJECTORY FILE
WRITING COORDINATES TO OUTPUT FILE AT STEP 100
CLOSING COORDINATE DCD FILE
WRITING VELOCITIES TO OUTPUT FILE AT STEP 100
==========================================
WallClock: 22.175739  CPUTime: 21.766689  Memory: 52056 kB
Program finished.