Re: Kb, Ktheta values for TIP3P water model

From: Kenno Vanommeslaeghe (
Date: Thu Jul 31 2014 - 17:28:09 CDT

On 07/31/2014 05:24 PM, JC Gumbart wrote:
> This is really good to know. Somehow that detail escaped me in the past.

I probably should have given the physical explanation right away in my
reply, but no harm is done, as Axel did a better job at it than I would
have done. :)

> This is funny, as Iím reading now about whether even a 4-fs time step is acceptable when using hydrogen mass repartitioning. My guess is you would say no? I read the namd-l discussion from a couple years ago in which Axel chose not to give an opinion then.

There seems to be a great deal of skepticism about this in the community.
I don't know much about these things, but I would not expect the amount of
_integrator_ artifacts in a 4fs time step simulation with 4amu hydrogens
to be greater than in a 2fs time step simulation with 1amu hydrogens.
Rather, the cause for concern would seem to be the _direct_ effect of the
heavier hydrogens on the dynamics of the system.

Experimentally, heavy water (with 2amu hydrogens) is known to inhibit cell
division and cause death, but that may have to do with proton mobility,
which we're not capturing in regular MD simulations anyhow. Also,
real-life deuteration increases the total mass of the molecule so it's not
the same as repartitioning. In the end, only systematic comparative
simulations will tell (I probably need to brush up on my literature there).

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:04 CST