[gmx-users] TIP4P molecules stuck together
johnwhittake at zedat.fu-berlin.de
Thu May 9 16:43:15 CEST 2019
I have a rather strange question that I hope someone can shed some light on.
Before I begin, I want to note that I am pioneering some new developments
of the Adaptive Resolution Simulation technique
(https://doi.org/10.1002/adts.201900014), so the simulations/techniques I
am performing/implementing are fairly non-standard with respect to normal
With that in mind, I am simulating a box of TIP4P water and calculating
structural/static properties. My simulations utilize a force-cap of 2000
kJ/(mol nm) at each time step - i.e., when the force on an atom is larger
than +/- 2000, the force is automatically normalized to +/- 2000 to
prevent explosive forces due to atomic overlaps.
For the most part, this works for the purposes of my simulations but I
have observed some water molecules "sticking" together in the
configuration shown here:
with a corresponding O-H radial distribution function (unnormalized) shown
where there is a clear (albeit, small) probability of finding a hydrogen
atom an extremely short distance from an oxygen.
The molecules travel together like this for several ps and then, for
seemingly no reason, split apart and carry on perfectly fine for the rest
of the simulation.
I have performed a single-point energy calculation on this configuration
in vacuum and have found, as one would expect, the forces on each atom are
massive (on the order of 10^7). Yet, the molecules do not repel and seem
to prefer this configuration for a short time.
I have a feeling that this configuration is allowed when the forces are
normalized to 2000 and the molecules become trapped there.
I am wondering if anyone may have some experience with TIP4P water
molecules taking on unphysical configurations for non-negligible times. I
have not tried this same simulation using TIP3P yet, so I'm unsure if it
has something to do with electrostatic interactions with the virtual site,
but I will test this tomorrow.
Thank you for any information/speculation/guesses as to why this is
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