From: raghav singh (raghavbioinfo_at_gmail.com)
Date: Mon Mar 05 2012 - 08:12:33 CST
Hello All,
I am trying to run SMD simulation on ssDNA... but getting this ( ABNORMAL
EOF FOUND - buffer=*END*) error. I have already looked through archives and
there is no satisfactory suggestion is posted.
if the guys who already gone through these problems have any suggestion or
solution ... Please suggest me.
Thank You
Raghav
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 10
Info: LOAD BALANCER Centralized
Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
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: MIN ATOMS PER PATCH 40
Info: INITIAL TEMPERATURE 300
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME single_ww_pcv.dcd
Info: DCD FREQUENCY 500
Info: DCD FIRST STEP 500
Info: XST FILENAME single_ww_pcv.xst
Info: XST FREQUENCY 500
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME single_ww_pcv
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME single_ww_pcv.restart
Info: RESTART FREQUENCY 500
Info: BINARY RESTART FILES WILL BE USED
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 0.48
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 16.48
Info: ENERGY OUTPUT STEPS 100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000
Info: PRESSURE OUTPUT STEPS 100
Info: FIXED ATOMS ACTIVE
Info: SMD ACTIVE
Info: SMD VELOCITY 0.005 ANGSTROM/TIMESTEP
Info: SMD DIRECTION -0.0259491 0.998205 0.0539723
Info: SMD K 7
Info: SMD K2 0
Info: SMD OUTPUT FREQUENCY 10 TIMESTEPS
Info: SMD FILE smd1_ww_eq.ref
Info: 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 300 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 0 0 0
Info: CELL FLUCTUATION IS ISOTROPIC
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 1330956154
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB smd1_ww_eq.pdb
Info: STRUCTURE FILE smd1_autopsf.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS par_all27_prot_na.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
FATAL ERROR: ABNORMAL EOF FOUND - buffer=*END*
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