ERROR: Constraint failure in RATTLE algorithm for atom 474!

From: suresh satpati (satpatisuresh_at_gmail.com)
Date: Tue Apr 09 2013 - 00:54:41 CDT

Dear Sir,
I m facing problem in running simulation for dna. i have got following
errors for which some solutions in NAMD mailing list is available (as to
check atom 474 velocity, it might be colliding with nearest atom). but i
don't know how to do that. plz let me know how to do that by using which
tool i have to do and how to do. plz forward some tutorial link or guidance
if possible.

amber on
ambercoor dna.inpcrd
parmfile dna.prmtop
temperature 0

outputEnergies 500
outputTiming 500
outputPressure 500
xstFreq 500
dcdFreq 500
restartfreq 50000
wrapAll on
wrapWater on
wrapNearest on

rigidBonds all
timestep 2
nonBondedFreq 1
fullElectFrequency 2
stepsPerCycle 20

switching on
switchDist 10.5
cutoff 12
pairlistdist 13.5

cellBasisVector1 64.688 00.000 00.000
cellBasisVector2 00.000 59.714 00.000
cellBasisVector3 00.000 00.000 59.789
cellOrigin 33.659 31.476 31.505

# the margin could be reduced once the cell is equilibrated
margin 5

Pme on
PmeGridsizeX 70
PmeGridsizeY 60
PmeGridsizeZ 60

exclude scaled1-4
1-4scaling 1.0

fixedAtoms on
fixedAtomsForces on
fixedAtomsFile dna_fix_backbone.pdb
fixedAtomsCol B

constraints on
consRef dna_restraint.pdb
consKFile dna_restraint.pdb
consKCol B

langevin on
langevinDamping 10
langevinTemp 310
langevinHydrogen no

langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay 100
langevinPistonTemp 310

useGroupPressure yes # smaller fluctuations
useFlexibleCell yes # allow dimensions to fluctuate
independently
useConstantRatio yes # fix shape in x-y plane

binaryoutput off
outputname dna_eq

# run one step to get into scripting mode
minimize 0

# turn off until later
langevinPiston off

# minimize nonbackbone atoms
minimize 40000
output min_fix

# min all atoms
fixedAtoms off
minimize 40000
output min_all

set temperature 10
#gradually heating
for {set i 10} {$i <= 310} {incr i 30} {
langevinTemp $i
run 10000
output heat_$i
}

# heat with CAs restrained

run 50000
output heat

# equilibrate volume with CAs restrained
langevinPiston on
run 50000
output equil_ca

# equilibrate volume without restraints 1000ps
constraintScaling 0
run 500000

ERROR: Constraint failure in RATTLE algorithm for atom 474!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.

-- 
*Regards,
Suresh Satpati*

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