AMBER Archive (2008)

Subject: AMBER: Hydroxide ion in POL3 water

From: D.J. Cole (
Date: Thu Dec 18 2008 - 06:13:58 CST


I am attempting to reproduce simulations of polarizable hydroxide ions in
the POL3 water model using Amber10. I have 5 hydroxide ions (and 5 Na+
counter-ions) and a frozen surface in a water box of size approximately 35
A^3. All parameters are taken from Phys. Chem. Chem. Phys. 10, 4975 (2008),
where the authors successfully simulate this system using Amber8.

After heating, the simulation usually ends after about 30ps of
equilibration with the following error message:

vlimit exceeded for step 38539; vmax = 26.6469
vlimit exceeded for step 38540; vmax = **********

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 5 1 449 450

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

By checking the trajectory, the O of the hydroxide ion gets too close to a
H of water. The induced dipole of this O atom gets very large (polarization
catastrophe I think). The ion is not at the surface, so this has no effect.
My frcmod file for the hydroxide ion and input file for equilibration are
below. I would be grateful if anyone can spot why I'm unable to reproduce
this simulation (note that I can increase the time to failure by decreasing
diptol, but the computation time gets very long).

This is the parameter set for OH-
OM 16.0 1.800
HM 1.008 0.000
OM-HM 320.0 1.0000


  OM 2.155 0.150
  HM 0.0 0.0

  cut=10.0, ntb=1,
  ntpr=1000, ntwx=1000,
  ntt=1, tautp=2.0,
  ipol=1, iwrap=1,
  ibelly=1, bellymask=':449-2012'
RES 449

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