PROTEIN VACUUM MINIMIZATION ERROR

From: Semorale (semorale_at_gmail.com)
Date: Sat May 24 2008 - 10:24:47 CDT

Hello NAMD users!

I want to make a vacuum minimization for a protein of 15000 atoms, with fix
protein backbone. I tried several configurations, but in all appears this
error for the same hydrogen atom:

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 11000
ERROR: Atom 5211 velocity is 32723.6 20404.1 21559.3 (limit is 12000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Exiting prematurely.

I have reviewed the DCD and apparently did not see anything strange ... *how
could solve this?*
*Reply please!!*
Thanks you very much for yours great help!!

SAMUEL.

*my last configuration:*

# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.prm
#parameters par-extraterms.inp
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12
switching on
switchdist 10
pairlistdist 14

# Integrator Parameters
timestep 1.0 ;# 1fs/step (2)
rigidBonds none ;# needed for 1fs steps (2)
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20

# Constant Temperature Control
langevin off ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 10/ps (5)
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens

# use lighter damping now that system is equilibrated
# 0 para NVT 1 para NPT
if {0} {
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay 100
langevinPistonTemp $temperature
}

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

# Periodic Boundary Conditions
#cellBasisVector1 133.2 0.0 0.0
#cellBasisVector2 0.0 132.3 0.0
#cellBasisVector3 0.0 0.0 97.2
#cellOrigin -0.38 -0.59 0.66
# the z dimension is going to shrink so pad sufficiently
# the margin could be reduced once the cell is equilibrated
margin 3

#wrapAll on
#wrapNearest on
# PME (for full-system periodic electrostatics)
#PME yes
#PMEGridSizeX 120
#PMEGridSizeY 120
#PMEGridSizeZ 120

# Output
binaryoutput no
outputEnergies 500
outputTiming 500
xstFreq 1000
dcdFreq 1000
restartfreq 1000

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

if {1} {
fixedAtoms on
fixedAtomsForces yes
fixedAtomsFile fix.pdb
fixedAtomsCol B
}

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

if {0} {
constraints on
consRef restrain_CA.pdb
consKFile restrain_CA.pdb
consKCol 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?
}

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

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

# run one step to get into scripting mode
minimize 0
# turn off until later
langevinPiston off
#fixedAtoms off
# minimize nonbackbone atoms

minimize 5000
output min_fixBB_vacio
run 250000

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