From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Tue Jul 19 2011 - 13:39:37 CDT

 Dear NAMD Users:
I am working with a cationic amphiphilic peptide named Bactenecin whose linear sequence is RLCRIVVIRVCR. I worked with the peptide in a water sphere. There was no problems in minimization and warming the system, but during the equilibration the peptide tends to go outside the water sphere. I believe it is not normal. Does anybody know how to avoid it?
The script I used for the euilibritaion was:
structure ../Estructuras/bact.psf
coordinates ../Estructuras/bact.pdb
bincoordinates ../Calentamiento300/bact_cal300.coor
binvelocities ../Calentamiento300/bact_cal300.vel
set outputname bact_eq
firsttimestep 0

paraTypeCharmm on
parameters ../Estructuras/par_all22_prot.inp

exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 8.
pairlistdist 13.5
margin 0
# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds all ;# needed for 1fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
# Output
outputName $outputname
dcdfreq 1000
outputEnergies 100

# Boundary conditions
extendedSystem ../Calentamiento300/bact_cal300.xsc
wrapWater on
# Spherical boundary conditions
sphericalBC on
sphericalBCcenter 1.272152066230774 -0.23037071526050568 -0.2613491117954254
sphericalBCr1 23.563667210382658
sphericalBCk1 10
sphericalBCexp1 2
# Restrains
fixedAtoms on
fixedAtomsCol B
fixedAtomsForces on
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp 300
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Equilibración
run 2000000

I wait that someone can help me with this.
Thanks for your help.
 Hernán Andrés Morales Navarrete

Biophysics and Molecular Modeling Group
Physics Department
Escuela Politécnica Nacional, Quito - Ecuador
Ladrón de Guevara E11-253.
Casilla 17-01-1253


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