error in scripting

From: ipsita basu (ibasu788_at_gmail.com)
Date: Mon Nov 16 2009 - 00:47:57 CST

Dear all,
  This is my config file:
#JOB DESCRIPTION ##
#############################################################

# mem system

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure min_mem.psf
coordinates min_mem.pdb
#binvelocities min_mem.vel

set start_temperature 0
set hold_temperature 298
set outputname min_mem.md

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters ./p.prm
temperature 0

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0 #Cutoff-2
pairlistdist 14.0 #Cutoff+2
stepspercycle 10
margin 2.5

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
useSettle on ;#If rigid bonds are enabled use
#non-interactive SETTLE alg to keep waters rigid

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinHydrogen no ;# don't couple langevin bath to hydrogens
#langevinTemp $hold_temperature ;#langevin temperature is
#defined in protocol section

#Affects the output. Wrapping does not affect the simulation.
wrapWater on
wrapAll on

#Pressure Control
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp 298

# Periodic Boundary Conditions
cellBasisVector1 65.02 0 0
cellBasisVector2 0 61.95 0
cellBasisVector3 0 0 103.53
cellOrigin 0.0 0.0 0.0

#PME (for full-system periodic electrostatics)
PME yes
#PMEGridSpacing 1.0 ;#Using good default. Let NAMD set the grid.

PMEGridSizeX 72
PMEGridSizeY 64
PMEGridSizeZ 108

# Output
outputName ipout

restartfreq 2500
dcdfreq 2500
xstFreq 2500
outputEnergies 2500
outputPressure 2500

#############################################################
## EXTRA PARAMETERS ##
#############################################################

#constraints on

#############################################################

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
#minimize 5000

#RELAXATION PROTOCOL
# 350000 steps
# 140 frames (dcdfreq=2500)
# 700 ps (timestep=2fs)

# Heat +1K in 0.4ps
for { set TEMP 0 } { $TEMP < 298 } {
incr TEMP 1 } {
       langevinTemp $TEMP
       reinitvels $TEMP
       run 200
}

#Adjust environment to final conditions
langevinTemp 298
reinitvels 298

#Constraints release protocol

#Free dynamics for 10ns
#constraintScaling 0
run 5000000

And the name of my config file is ip. I run this by this command ./namd2 ip

My error message is:
Charm++: standalone mode (not using charmrun)
Info: NAMD 2.6 for Linux-i686
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 50900 for net-linux
Info: Built Tue Sep 8 11:20:07 IST 2009 by cm on Chemistry-Server
Info: 1 NAMD 2.6 Linux-i686 1 Chemistry-Server cm
Info: Running on 1 processors.
Info: 7244 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Changed directory to ../../mem
Info: Configuration file is gt
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 10
Info: PERIODIC CELL BASIS 1 65.02 0 0
Info: PERIODIC CELL BASIS 2 0 61.95 0
Info: PERIODIC CELL BASIS 3 0 0 103.53
Info: PERIODIC CELL CENTER 0 0 0
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 2000 steps
Info: FIRST LDB TIMESTEP 50
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS 50
Info: MAX PAIR PARTITIONS 20
Info: SELF PARTITION ATOMS 125
Info: PAIR PARTITION ATOMS 200
Info: PAIR2 PARTITION ATOMS 400
Info: MIN ATOMS PER PATCH 100
Info: INITIAL TEMPERATURE 0
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: DCD FILENAME gtout.dcd
Info: DCD FREQUENCY 2500
Info: DCD FIRST STEP 2500
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME gtout.xst
Info: XST FREQUENCY 2500
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME gtout
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME gtout.restart
Info: RESTART FREQUENCY 2500
Info: BINARY RESTART FILES WILL BE USED
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 2500
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 25000
Info: PRESSURE OUTPUT STEPS 2500
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 0
Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
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 298 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 0 0 0
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 72 64 108
Info: PME MAXIMUM GRID SPACING 1.5
Info: Attempting to read FFTW data from FFTW_NAMD_2.6_Linux-i686.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.6_Linux-i686.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 1258354263
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB min_mem.pdb
Info: STRUCTURE FILE min_mem.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS ./p.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 98 BONDS
Info: 253 ANGLES
Info: 285 DIHEDRAL
Info: 41 IMPROPER
Info: 0 CROSSTERM
Info: 50 VDW
Info: 0 VDW_PAIRS
Warning: Ignored 4020 bonds with zero force constants.
Warning: Will get H-H distance in rigid H2O from H-O-H angle.
FATAL ERROR: Atom 70 has bad group size. Check for duplicate bonds.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Atom 70 has bad group size. Check for duplicate bonds.

Stack Traceback:
  [0] [0x82f7632]
  [1] [0x8048762]
  [2] [0x81f22c2]
  [3] [0x81f6a8f]
  [4] [0x81fc062]
  [5] [0x8207909]
  [6] [0x8248c6a]
  [7] [0x824beb7]
  [8] [0x830f9e8]
  [9] [0x83299d0]
  [10] [0x8310393]
  [11] [0x831524e]
  [12] [0x8344451]
  [13] [0x8344ade]
  [14] [0x833c78a]
  [15] [0x824b52d]
  [16] [0x804ba19]
  [17] [0x8408808]
  [18] [0x8048121]
Charm++ fatal error:
FATAL ERROR: Atom 70 has bad group size. Check for duplicate bonds.

Aborted
Please help me. What is the solution of this problem? I am very new to namd.
I really need your help.

-- 
Ipsita Basu
Research Fellow
c/o : Dr. Chaitali Mukhopadhyay
Rajabazar Science College
92 APC Road
Kolkata - 700009

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