error during heating of the minimized system: (please reply!)

From: Falgun Shah (fhshah_at_olemiss.edu)
Date: Wed Jan 14 2009 - 01:08:28 CST

Dear sir

i am doing minimization and equilibration of protein of interest. I have
minimized sysem for 1500 steps of CG minimization using backbone and calpha
atom fixed

In following step, i want to heat the system in increment (0 to 300k for
3000 steps: 100K for 1000steps). i am getting following error:

ERROR: Step 130 cell rescaling factor limited.
ERROR: Constraint failure in RATTLE algorithm for atom 2822!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.

I am pasting my configuration file

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

structure junk_wb_ionized.psf
coordinates junk_wb_min_calpha2_eq.coor

set temperature 0
set outputname junk_wb_heat_calpha_eq

set temp_step 20
firsttimestep 0

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

# Input
paraTypeCharmm on
parameters
/home/Amber9.0/NAMD_2.6_Linux-amd64/namd-tutorial-files/common/par_all27_prot_lipid.inp

temperature $temperature

# Periodic Boundary Conditions
#
if {1} {
cellBasisVector1 95.4 0. 0.
cellBasisVector2 0. 75.58 0.
cellBasisVector3 0. 0. 65.72
cellOrigin 10.2 1.2 1.3
}
wrapWater on
wrapAll on

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 13.
switching on
switchdist 11.
pairlistdist 14.5

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20

# PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSizeX 125
PMEGridSizeY 81
PMEGridSizeZ 64
}

# temp rescaling actually brings the temp down
# thats why perform incremental heating

if {1} {
reassignTemp $temp_step ;#starting temp
reassignIncr $temp_step ;#temp increment
reassignHold 300 ;#final temp
reassignFreq 100 ;#num timestep to temp incr.

# Constant Temperature Control
#langevin off ;# do langevin dynamics
#langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
#langevinTemp $temperature
#langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Use BerendsenPressure Control to equilibrate
if {1} {
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

BerendsenPressure on
BerendsenPressureTarget 1.01325 ;# in bar -> 1 atm
BerendsenPressureCompressibility 4.57E-5
BerendsenPressureRelaxationTime 200
BerendsenPressureFreq 20
}

# Output
outputName $outputname

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 50
outputPressure 100
binaryoutput no ;# give me the pdb instead of the .coor

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

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

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

# Minimization
if {1} {
minimize 100
reinitvels $temperature
}
run 3000 ;# 5ps

Please let me know if there is any error in my configuration file.

Thanks

-- 
Falgun H shah
PhD candidate (3rd year)
Department of Medicinal Chemistry
2028, Natural Product Center
University of Mississippi
Ph No: 6629151286(O)
          662 801 5667(M)
email: fhshah_at_olemiss.edu

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