Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration

From: Roy Fernando (roy.nandos_at_gmail.com)
Date: Sun Jul 15 2012 - 17:13:22 CDT

Dear All,

I try to simulate my test system containing two Neon atom under Generalized
Born Implicit Solvent Technique.
I did not use any charge.
At the end of the equilibration, I observe that the atoms are missing.
I used the basic configuration file came with the tutorial. (posted below).
I will appreciate if someone can give some insight on how I can keep the
atoms confined to a certain volume. Or is it not possible in this method?

regards,

Roy

#############################################################
## JOB DESCRIPTION ##
#############################################################

# Minimization and Equilibration of
#Neon atoms in generalized Born implicit solvent

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

structure NE2-1.psf
coordinates NE2-1.pdb

set temperature 310
set outputname NE2_gbis_eq

firsttimestep 0

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

# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
temperature $temperature

# Implicit Solvent
gbis on
alphaCutoff 2.0
ionConcentration 0.0

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 4.0
switching on
switchdist 3.0
pairlistdist 6.0

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Output
outputName $outputname

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100

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

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

# Minimization
minimize 1000
reinitvels $temperature

run 25000 ;# 5ps

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