Hi,
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-
MASS
OM 16.0 1.800
HM 1.008 0.000
BOND
OM-HM 320.0 1.0000
ANGLE
DIHE
NONBON
OM 2.155 0.150
HM 0.0 0.0
hydroxide
&cntrl
imin=0,irest=1,ntx=5,
nstlim=200000,dt=0.001,
ntc=2,ntf=2,
cut=10.0, ntb=1,
ntpr=1000, ntwx=1000,
ntt=1, tautp=2.0,
temp0=300.0,
ipol=1, iwrap=1,
ibelly=1, bellymask=':449-2012'
/
&ewald
indmeth=1,
diptol=0.00000001,
dipmass=0.33,
maxiter=50,
scaldip=0,
/
&dipoles
Group1
RES 449
END
END
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Received on Fri Dec 19 2008 - 01:17:07 PST
