Re: Kb, Ktheta values for TIP3P water model

From: Axel Kohlmeyer (
Date: Thu Jul 31 2014 - 14:14:43 CDT

On Thu, Jul 31, 2014 at 3:03 PM, Kenno Vanommeslaeghe
<> wrote:
> It's slightly more complicated than that. Strictly spoken, even with SHAKE,
> a 2fs time step is too long if you want sensitive bulk phase properties to
> converge (as a function of the time step) within a few %. In line with this,
> the bulk phase simulations we perform to optimize the nonbonded parameters
> are done with SHAKE on all covalent bonds involving hydrogens (the
> equivalent to "rigidBonds all" in NAMD) *and* a 1fs time step, so that would
> be the most rigorously correct use of the force field. The CHARMM community
> is a bit divided over whether it's justified to use a 2fs time step. The
> prevalent opinion on our lab is that it almost never significantly alters
> the properties of interest in typical biomolecular simulations, so we use
> 2fs for most of our biomolecular work. Other labs default to 1fs. However,
> we all agree(*) on two things:
> - for very fine quantitative work (such as force field parametrization but
> also certain detailed studies of lipid membrane properties), 1fs is the
> standard
> - no matter whether using 1fs or 2fs, "SHAKE BONH" / "rigidBonds all" should
> always be applied (If the methodology/software allows for it. The BOND
> parameters provide a workaround/safety net if it doesn't, but at the price
> of some accuracy with respect to the parametrization.)

there is a simple way to rationalize this: a water model with flexible
bonds/angles is on average somewhat deformed with respect to the
reference bond length or angle used for the constraint. as a
consequence, water molecules in the condensed form will become
polarized. that would have to be corrected for in the
parameterization. of course, this applies to all bonds involving
hydrogen atoms, but the effect is by far the most pronounced for water


> (*) famous last words

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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