Re: namd job crashed

From: snoze pa (snoze.pa_at_gmail.com)
Date: Mon Feb 01 2010 - 11:26:42 CST

Please post the last 10 lines of your log file not the first one..

On Mon, Feb 1, 2010 at 10:55 AM, Bala subramanian
<bala.biophysics_at_gmail.com> wrote:
> 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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