From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Dec 27 2009 - 08:47:12 CST
Hello:
I wonder whether I am using a wrong force field or bad tuning for the
equilibration of a CG protein-bilayer-waterbox. I have already
restarted 4 times. Every 15,000 steps, or so, the simulation crashes,
each time for atoms (beads) moving too fast, each time for different
protein beads, sometimes also involving a water bead lying in the same
region, sometimes also complaining "Bad global exclusion count
errors", initially also complaining that the "periodic cell has become
too small". Always the extracellular portion of the protein is
involved, never - so far - the pore region, which is embedded in a
bilayer. To a novice for namd it looks like a problem with the force
field.
Settings:
margin 25
paraTypeCharmm on
set temperature 310
# temperature $temperature
# Periodic Boundary Conditions!
if {0}
# Force-Field Parameters
exclude 1-2
cutoff 12.0
switching on
switchdist 9.0
pairlistdist 16.0 ;# cutoff +4
hgroupcutoff 0
# Integrator Parameters
timestep 20.0 ;# 20fs/step
rigidBonds no ;# only needed for all-atoms
nonbondedFreq 1 ;# nonbonded forces every step
fullElectFrequency 2 ;# PME only every other step
stepspercycle 20 ;# redo pairlist every twenty steps
#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSizeX 134
PMEGridSizeY 168
PMEGridSizeZ 137
}
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# (ps^-1) damping coefficient (gamma) used
by Freddolino et al
langevinTemp $temperature ;# random noise at this level
langevinHydrogen no ;# don't couple bath to hydrogens
# Constant Pressure Control (variable volume)
if {1} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 1000 ;# (fs)
langevinPistonDecay 500 ;# (fs)
langevinPistonTemp $temperature
}
# Fixed Atoms Constraint (set PDB beta-column to 1)
if {0}
# Minimization
if {1} {
minimize 10000
reinitvels $temperature
}
run 25000 ;# 500 ns
Thanks for any suggestion
francesco pietra
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