this will go into the log file. mysystem_heat.coor
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE   mysystem_heat.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               1
Info: NUMBER OF STEPS        0
Info: STEPS PER CYCLE        20
Info: PERIODIC CELL BASIS 1  131 0 0
Info: PERIODIC CELL BASIS 2  0 30.1 0
Info: PERIODIC CELL BASIS 3  0 0 36.5
Info: PERIODIC CELL CENTER   -44.2146 2.38894 2.11828
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
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: VELOCITY FILE          mysystem_heat.vel
Info: CENTER OF MASS MOVING? NO
Info: DIELECTRIC             1
Info: EXCLUDE                SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR       1
Info: DCD FILENAME           mysystem_pr.dcd
Info: DCD FREQUENCY          1000
Warning: INITIAL COORDINATES WILL NOT BE WRITTEN TO DCD FILE
Info: XST FILENAME           mysystem_pr.xst
Info: XST FREQUENCY          1000
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME        mysystem_pr
Info: RESTART FILENAME       mysystem_pr_restart
Info: RESTART FREQUENCY      10000
Info: RESTART FILES WILL NOT BE OVERWRITTEN
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                 1
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        17
Info: ENERGY OUTPUT STEPS    1000
Info: TIMING OUTPUT STEPS    1000
Info: PRESSURE OUTPUT STEPS  1000
Info: FIXED ATOMS ACTIVE
Info: FORCES BETWEEN FIXED ATOMS ARE CALCULATED
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   300
Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
Info: LANGEVIN DYNAMICS 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 100 FS
Info:     PISTON TEMPERATURE IS 300 K
Info:       PRESSURE CONTROL IS GROUP-BASED
Info:    INITIAL STRAIN RATE IS 0 0 0
Info:       CELL FLUCTUATION IS ISOTROPIC
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE               1e-006
Info: PME EWALD COEFFICIENT       0.257952
Info: PME INTERPOLATION ORDER     4
Info: PME GRID DIMENSIONS         64 64 64
Info: Attempting to read FFTW data from FFTW_NAMD_2.5_Win32-i686.txt
Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
Info: Writing FFTW data to FFTW_NAMD_2.5_Win32-i686.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY      2
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     1121633328
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         mysystem_heat.coor
Info: STRUCTURE FILE         mysystem.psf
Info: PARAMETER file: CHARMM format! 
Info: PARAMETERS             par_all27_prot_na.prm
Info: SUMMARY OF PARAMETERS:
Info: 250 BONDS
Info: 622 ANGLES
Info: 1049 DIHEDRAL
Info: 73 IMPROPER
Info: 130 VDW
Info: 0 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 12051 ATOMS
Info: 9452 BONDS
Info: 10257 ANGLES
Info: 11153 DIHEDRALS
Info: 731 IMPROPERS
Info: 0 EXCLUSIONS
Info: 1069 FIXED ATOMS
Info: 32946 DEGREES OF FREEDOM
Info: 4702 HYDROGEN GROUPS
Info: 547 HYDROGEN GROUPS WITH ALL ATOMS FIXED
Info: TOTAL MASS = 76853.2 amu
Info: TOTAL CHARGE = -18 e
Info: *****************************
Info: Entering startup phase 0 with 0 kB of memory in use.
Info: Entering startup phase 1 with 0 kB of memory in use.
Info: Entering startup phase 2 with 0 kB of memory in use.
Info: Entering startup phase 3 with 0 kB of memory in use.
Info: PATCH GRID IS 7 (PERIODIC) BY 1 (PERIODIC) BY 2 (PERIODIC)
Info: REMOVING COM VELOCITY -0.0389633 0.0204912 0.0533061
Info: LARGEST PATCH (0) HAS 950 ATOMS
Info: Entering startup phase 4 with 0 kB of memory in use.
Info: PME using 1 and 1 processors for FFT and reciprocal sum.
Creating Strategy 4
Creating Strategy 4
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 0 kB of memory in use.
Info: Entering startup phase 6 with 0 kB of memory in use.
Info: Entering startup phase 7 with 0 kB of memory in use.
Info: COULOMB TABLE R-SQUARED SPACING: 0.0625
Info: COULOMB TABLE SIZE: 769 POINTS
Info: NONZERO IMPRECISION IN COULOMB TABLE: 2.52435e-029 (756) 1.57772e-029 (741)
Info: NONZERO IMPRECISION IN COULOMB TABLE: 8.47033e-022 (760) 1.05879e-021 (754)
Info: Entering startup phase 8 with 0 kB of memory in use.
Info: Finished startup with 0 kB of memory in use.
TCL: Running for 30000 steps
PRESSURE: 0 -5466.46 879.986 -2185.7 -4349.23 -158.677 -2096.15 3845.95 -425.799 1802.11
GPRESSURE: 0 -7716.6 1028.44 -2064.04 -4291.63 -2126.24 -2314.89 3896.94 -520.416 119.113
ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP               ELECT            VDW       BOUNDARY           MISC        KINETIC               TOTAL           TEMP         TOTAL2         TOTAL3        TEMPAVG            PRESSURE      GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG

ENERGY:       0      3769.9836      3635.3432      1339.3202       128.9822         -38383.0648      2239.9927         0.0000         0.0000      9842.9772         -17426.4657       300.6867    -17289.5929    -17289.5929       300.6867          -1274.3407     -3241.2421    143923.1500     -1274.3407     -3241.2421

OPENING EXTENDED SYSTEM TRAJECTORY FILE
ERROR: Atom 23 velocity is -2.18927e+006 3.44795e+006 -1.94734e+006 (limit is 10000)
ERROR: Atom 25 velocity is 5.01129e+006 -8.06707e+007 -1.19661e+008 (limit is 10000)
ERROR: Atom 354 velocity is -3811.67 8537.56 6265.98 (limit is 10000)
ERROR: Atom 371 velocity is 11016.2 -20372.4 35855.9 (limit is 10000)
ERROR: Atom 373 velocity is 13448.2 -2498.02 1389.83 (limit is 10000)
ERROR: Atom 386 velocity is 28403.5 -35127 -519408 (limit is 10000)
ERROR: Atom 475 velocity is 224196 -132825 -836272 (limit is 10000)
ERROR: Atom 490 velocity is -4.40048e+007 -4.41762e+007 7.62131e+007 (limit is 10000)
ERROR: Atom 783 velocity is 9420.1 12809.4 -6911.9 (limit is 10000)
ERROR: Atom 785 velocity is -1.64146e+009 1.28106e+009 6.44428e+008 (limit is 10000)
ERROR: Atom 798 velocity is -4.94361e+006 -1.30109e+007 -1.17203e+006 (limit is 10000)
ERROR: Atom 841 velocity is 7.0632e+008 -1.29977e+009 3.43386e+008 (limit is 10000)
ERROR: Atom 1121 velocity is -20559.8 -85611 25410.7 (limit is 10000)
ERROR: Atom 1139 velocity is 1.34865e+011 4.43213e+010 6.21894e+010 (limit is 10000)
ERROR: Atom 4948 velocity is 188239 498534 -266812 (limit is 10000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 292 velocity is 13972.1 10158.8 15048.7 (limit is 10000)
ERROR: Atom 337 velocity is 2.35904e+007 -1.52023e+007 1.19717e+007 (limit is 10000)
ERROR: Atom 516 velocity is 3.92437e+008 1.63369e+008 -1.50085e+008 (limit is 10000)
ERROR: Atom 565 velocity is 9141.03 175.587 -7434.85 (limit is 10000)
ERROR: Atom 575 velocity is 11579.7 -5772.05 -4967.29 (limit is 10000)
ERROR: Atom 612 velocity is 409965 62782.6 -400775 (limit is 10000)
ERROR: Atom 641 velocity is 1.05999e+006 -1.70975e+006 -1.00363e+006 (limit is 10000)
ERROR: Atom 654 velocity is 35899.1 -11547 -32692.8 (limit is 10000)
ERROR: Atom 682 velocity is 18798.8 -15672.7 -16338 (limit is 10000)
ERROR: Atom 686 velocity is 40912.3 7066.59 542.369 (limit is 10000)
ERROR: Atom 730 velocity is 158908 178296 33884.2 (limit is 10000)
ERROR: Atom 880 velocity is 2.14479e+007 -4.57834e+007 1.22806e+007 (limit is 10000)
ERROR: Atom 1094 velocity is 1.28036e+007 2.73827e+006 -6.27038e+006 (limit is 10000)
ERROR: Atom 6280 velocity is 17380.7 -5454.34 -404.505 (limit is 10000)
ERROR: Atom 6282 velocity is 9334.35 -5082.78 -14198.6 (limit is 10000)
ERROR: Atom 352 velocity is 81895.7 100274 12514.2 (limit is 10000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 3244 velocity is -96616.4 -73421.5 -44678.8 (limit is 10000)
ERROR: Atom 3249 velocity is -75007.6 -15989.7 -33936.3 (limit is 10000)
ERROR: Atom 3426 velocity is -390510 601424 1.73024e+006 (limit is 10000)
ERROR: Atom 3429 velocity is -16402.4 -14246.5 -6641.39 (limit is 10000)
ERROR: Atom 3499 velocity is -1.46746e+007 -5.02519e+006 7.25892e+006 (limit is 10000)
ERROR: Atom 3508 velocity is -39494.1 -3902.71 -5368.8 (limit is 10000)
ERROR: Atom 3537 velocity is -5.95542e+006 -1.82849e+006 1.30444e+006 (limit is 10000)
ERROR: Atom 3565 velocity is -8955.66 2695.03 -6855.11 (limit is 10000)
ERROR: Atom 3651 velocity is -810.087 16931.5 -579.3 (limit is 10000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 3434 velocity is 40965.9 58096 80112.2 (limit is 10000)
ERROR: Atom 3471 velocity is 9459.91 18137.7 24278.4 (limit is 10000)
ERROR: Atom 3473 velocity is -2.38144e+006 2.26067e+006 4.95208e+006 (limit is 10000)
ERROR: Atom 3687 velocity is -318518 71578.1 -160752 (limit is 10000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 59 velocity is -9149.6 -73858.8 139376 (limit is 10000)
ERROR: Atom 62 velocity is 365241 590392 138447 (limit is 10000)
ERROR: Atom 64 velocity is 6.38534e+006 3.01736e+006 579001 (limit is 10000)
ERROR: Atom 65 velocity is 2.76361e+006 -49924.7 -2.343e+006 (limit is 10000)
ERROR: Atom 66 velocity is 236912 197977 -151852 (limit is 10000)
ERROR: Atom 1202 velocity is -2658.43 13863.3 3522.28 (limit is 10000)
ERROR: Atom 1222 velocity is 5.60691e+006 -3.24667e+007 2.19586e+007 (limit is 10000)
ERROR: Atom 1224 velocity is 46449.6 82863.8 71272 (limit is 10000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 126 velocity is 153515 -36502.1 -580153 (limit is 10000)
ERROR: Atom 145 velocity is 10822.4 -11412.1 18767.4 (limit is 10000)
ERROR: Atom 189 velocity is 49384.1 20652.1 21821.1 (limit is 10000)
ERROR: Atom 1060 velocity is 13757.4 -161.464 1296.25 (limit is 10000)
ERROR: Atom 1070 velocity is 491051 -517729 -154795 (limit is 10000)
ERROR: Atom 1235 velocity is 2.09757e+010 9.24275e+009 2.07446e+009 (limit is 10000)
ERROR: Atom 1245 velocity is 193773 -406445 215792 (limit is 10000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 2827 velocity is -9179.48 4425.89 -25705.2 (limit is 10000)
ERROR: Atom 2916 velocity is -43002.8 6623.67 -2851.88 (limit is 10000)
ERROR: Atom 2918 velocity is 891.332 56464.5 11426.7 (limit is 10000)
ERROR: Atom 3106 velocity is -8978.76 31658.5 5247.36 (limit is 10000)
ERROR: Atom 3140 velocity is -22107.8 20414.8 -4376.85 (limit is 10000)
ERROR: Atom 3295 velocity is -479999 102152 114701 (limit is 10000)
ERROR: Atom 3303 velocity is -1436.82 -9458.19 -6519.18 (limit is 10000)
ERROR: Atom 3831 velocity is -1.11671e+006 -842702 1.2359e+006 (limit is 10000)
ERROR: Atom 3862 velocity is -4.8612e+006 -784964 1.18742e+006 (limit is 10000)
ERROR: Atom 3976 velocity is -191953 -94830.2 34405.8 (limit is 10000)
ERROR: Atom 3995 velocity is -64588.6 -47994.5 -20054.3 (limit is 10000)
ERROR: Atom 2923 velocity is -247319 1.27578e+006 496794 (limit is 10000)
ERROR: Atom 4019 velocity is -9.93891e+006 -1.50265e+007 -5.53055e+006 (limit is 10000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 2934 velocity is -1.57034e+006 -2.63375e+006 17982.6 (limit is 10000)
ERROR: Atom 2957 velocity is -5.44101e+006 1.78265e+006 -2.29126e+006 (limit is 10000)
ERROR: Atom 2958 velocity is -16938.6 -12907.3 -10451.1 (limit is 10000)
ERROR: Atom 2979 velocity is -61546.3 -7367.1 -2612.33 (limit is 10000)
ERROR: Atom 2980 velocity is -7.56843e+006 -1.2922e+007 1.41136e+006 (limit is 10000)
ERROR: Atom 3042 velocity is -477.03 10396.2 -667.992 (limit is 10000)
ERROR: Atom 3044 velocity is -196543 1.10819e+006 593848 (limit is 10000)
ERROR: Atom 3793 velocity is 18092.3 -41927.9 -28840 (limit is 10000)
ERROR: Atom 3794 velocity is -23002.3 10829.2 -8148.29 (limit is 10000)
ERROR: Atom 3795 velocity is -1.64633e+011 -6.38139e+010 -2.35798e+010 (limit is 10000)
ERROR: Atom 3825 velocity is -878058 297340 2.27166e+006 (limit is 10000)
ERROR: Atom 4021 velocity is 8350.47 -146024 -67653 (limit is 10000)
ERROR: Atom 4038 velocity is -173149 355750 371636 (limit is 10000)
ERROR: Atom 4060 velocity is -622803 323467 47922.3 (limit is 10000)
ERROR: Atom 4062 velocity is 27884.4 308.046 -77496.6 (limit is 10000)
ERROR: Atom 4076 velocity is 1.00984e+007 -2.77378e+007 5.82805e+006 (limit is 10000)
ERROR: Atom 4118 velocity is 31139.6 -1549.03 -14907.9 (limit is 10000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Exiting prematurely.
==========================================
WallClock: 24.625000  CPUTime: 24.625000  Memory: 0 kB
Program finished.