namd job crashed

From: Bala subramanian (bala.biophysics_at_gmail.com)
Date: Mon Feb 01 2010 - 10:55:23 CST

Friends,
I am simulating a protein with a topology file created with xleap of amber
program. So far i have run 1.5ns of simulation. When i continue the
simulation, NAMD stops by just telling the following error. I dnt understand
why it suddenly happens. Kindly write me what is going wrong.

Info: FULL ELEInfo: Running on 20 processors.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.102693 s
Info: 36648.9 MB of memory in use based on /proc/self/stat
Info: Configuration file is pr1
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE /home1/bala/AGO_NODNA/PR1.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 500000
Info: STEPS PER CYCLE 10
Info: PERIODIC CELL BASIS 1 99.5074 0 0
Info: PERIODIC CELL BASIS 2 -33.1694 93.8175 0
Info: PERIODIC CELL BASIS 3 33.1694 46.9087 81.2484
Info: PERIODIC CELL CENTER 51.907 51.677 52.0055
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING TO IMAGE NEAREST TO PERIODIC CELL CENTER.
Info: LOAD BALANCE STRATEGY New Load Balancers -- ASB
Info: LDB PERIOD 2000 steps
Info: FIRST LDB TIMESTEP 50
Info: LAST LDB TIMESTEP -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS 20
Info: MAX PAIR PARTITIONS 8
Info: SELF PARTITION ATOMS 154Info: MIN ATOMS PER PATCH 100
Info: VELOCITY FILE /home1/bala/AGO_NODNA/PR1.vel
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 /home1/bala/AGO_NODNA/PR2.dcd
Info: DCD FREQUENCY 1000
Info: DCD FIRST STEP 1000
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME /home1/bala/AGO_NODNA/PR2
Info: RESTART FILENAME /home1/bala/AGO_NODNA/rsrt
Info: RESTART FREQUENCY 500
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 2.5
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 19
Info: ENERGY OUTPUT STEPS 1000
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000Info: LANGEVIN PISTON PRESSURE CONTROL
ACTIVE
Info: TARGET PRESSURE IS 1.01325 BAR
Info: OSCILLATION PERIOD IS 100 FS
Info: DECAY TIME IS 50 FS
Info: PISTON TEMPERATURE IS 303 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 4.28085e-05 4.28085e-05 4.28085e-05
Info: CELL FLUCTUATION IS ISOTROPIC
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 108 108 108
Info: PME MAXIMUM GRID SPACING 1
Info: Attempting to read FFTW data from
FFTW_NAMD_2.7b2_Linux-Itanium-MPI-Altix.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.7b2_Linux-Itanium-MPI-Altix.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: RIGID BONDS TO HYDROGEN : ALL
Info: ERROR TOLERANCE : 1e-08
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED 1265063634
Info: USE HYDROGEN BONDS? NO
Info: Using AMBER format force field!
Info: AMBER PARM FILE /home1/bala/AGO_NODNA/ago_nodna.top
Info: COORDINATE PDB /home1/bala/AGO_NODNA/PR1.coor
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 (/home1/bala/AGO_NODNA/ago_nodna.top) ...
PARM file in AMBER 7 format
Warning: Encounter 10-12 H-bond term
Warning: Found 21556 H-H bonds.

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