Simulation in water sphere meet with a FATAL ERROR about Bad global exclusion count

From: Shulin Zhuang (shulin.zhuang_at_gmail.com)
Date: Sun Nov 04 2007 - 21:01:45 CST

Dear All,

I do equilibration MD simulation of protein in water sphere with NAMD2.6.
The protein is I27, 89 resiudes,pdb 1tit. I have once sucessfully do 1 ns
equilibration of I 27. However, when this time, I just delete the last
residue 89, when I run equilibration at 392 ns, the MD stops and give the
error information:FATAL ERROR: Bad global exclusion count! How can I tackle
this problem.

Here, I put my configuration file of equilibration MD. Wish anyone will help
me out of this problem. Great thanks. Following is the configuration file.
For this configuration file, I just use it to do 1 ns equlibration of I 27
without deleting residue 89.

#############################################################
## Production run MD run ##
## in Water Sphere ##
#############################################################

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

# molecular system
set MOL 1tit
structure ${MOL}_sol_ionize.psf

set outputname ${MOL}_prod
set prod_restart ${MOL}_prod_restart

# after heating system
set inprot ${MOL}_heat
coordinates ${inprot}.coor
velocities ${inprot}.vel
extendedSystem ${inprot}.xsc

set temperature 300 ;# initial temperature

# Continuing a job from the restart files
if {0} {
set inputname myinput
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature" entry
if you use this!
extendedSystem $inputname.xsc
}

firsttimestep 0

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

# Input
paraTypeCharmm on
parameters par_all27_prot_lipid_na.inp

# Spherical boundary conditions
sphericalBC on
sphericalBCcenter -1.9094337225 0.573376715183 0.0411463677883
sphericalBCr1 31.2752613824
sphericalBCk1 10
sphericalBCexp1 2

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 13.0
switching on
switchdist 10.0
pairlistdist 14.5

# Integrator Parameters
timestep 1.0 ;# 1fs/step
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20

# Constant Temperature Control
# A: for heating, use temperature reassignment
if {0} {
reassignFreq 500 ;# tuned to be suit 'natural' heating for system.
reassignTemp 25 ;# to start from 0 Kelvin, else always lagging by 25K.
reassignIncr 25
reassignHold $temperature
}

# B: for heating, Temperature coupling via Langevin dynamics
if {1} {
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# couple langevin bath to hydrogens
}

# Constant Pressure Control (variable volume)
if {0} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100
langevinPistonDecay 50
langevinPistonTemp $temperature
}

# for saving restart file
if {0} {
restartname $prod_restart
restartfreq 200 ;# 500steps = every 0.5ps
restartsave yes
binaryrestart yes ;# yes will preserves more accuracy.
}

# Output
outputName $outputname
dcdfreq 200
xstFreq 200
outputEnergies 100
outputTiming 100
binaryoutput yes

# Fixed Atoms Constraint (set PDB beta-column to 1)
if {0} {
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile fix_backbone.pdb
fixedAtomsCol B
}

# IMD Settings (can view sim in VMD)
if {0} {
IMDon on
IMDport 3000 ;# port number (enter it in VMD)
IMDfreq 1 ;# send every 1 frame
IMDwait no ;# wait for VMD to connect before running?
}

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

# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)

#constantforce yes
#consforcefile ../common/example-output/ubq_ww_eq2.ref

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

# Minimization
if {0} {
minimize 3000
}

run 1000000
#production for 1ns

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