From: prasun kumar (prasun30_at_gmail.com)
Date: Mon Feb 01 2010 - 12:00:49 CST
Plz unsubscribe me............
or sum1 plz tell me how to unsubscribe.......
thanx alot......
PRASUN (ASHOKA)
On Mon, Feb 1, 2010 at 10:59 PM, <gbellesia_at_chem.ucsb.edu> wrote:
> 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.
> >
>
>
>
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