From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Dec 27 2009 - 09:47:46 CST
On Sun, 2009-12-27 at 15:47 +0100, Francesco Pietra wrote:
> 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.
to me this sounds more like you have a very high
energy starting configuration.
multi-component systems are always tricky to equilibrate
without an elaborate protocol. as simple minimization and
then heating up to production usually is not sufficient.
i would suggest to first use position restraints (called
constraints in NAMD-speak, IIRC) to confine most of the
system and then let only parts equilibrate independently.
in case of very high potential energy environments, you
may need to alternate between minimization and MD a few
times. perhaps you equilibrate first the area away from
the protein, i.e. close the "gaps" between the periodic
images and let the bilayer "heal", and then pay attention
to the proximity of the protein. in any case you have to
make sure that you dissipate sound waves from the implosions
due to the solvation and embedding into the bilayer.
using a high friction coefficient in the langevin thermostat
certainly helps with that.
also i would use a reduced time step to improve
the stability of the MD integration and avoid
extremely close contacts of fast moving atoms.
there is no single automated way to do this right.
one has to use common sense and closely observe the
system to react to what is going on.
axel.
>
> 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
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com Institute for Computational Molecular Science College of Science and Technology Temple University, Philadelphia PA, USA.
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