From: gbellesia_at_chem.ucsb.edu
Date: Mon Feb 01 2010 - 11:29:33 CST
Hi, take a look here ... Caveat 2 ...
http://www.ks.uiuc.edu/Research/namd/2.7b2/ug/node14.html
-g
> 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.
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:55:23 CST