[gmx-users] mdrun-adjusted cutoffs?!

[Mark Abraham]

Hi,

Zero, because we are shifting between equivalent ways to compute the total
electrostatic interaction.

You can turn off the PME tuning with mdrun -notunepme, but unless there's a
bug, all that will do is force it to run slower than optimal. Obviously you
could try it and see that the FE of hydration does not change with the
model, so long as you have a reproducible protocol.

Mark


On Fri., 7 Dec. 2018, 06:39 Alex <nedomacho at gmail.com wrote:

> I'm not ignoring the long-range contribution, but yes, most of the
> effects I am talking about are short-range. What I am asking is how much
> the free energy of ionic hydration for K+ changes in, say, a system that
> contains KCl in bulk water -- with and without autotuning. Hence also
> the earlier question about being able to turn it off at least temporarily.
>
> Alex
>
> On 12/6/2018 5:42 AM, Mark Abraham wrote:
> > Hi,
> >
> > It sounds like you are only looking at the short-ranged component of the
> > electrostatic interaction, and thus ignoring the way the long range
> > component also changes. Is the validity of the PME auto tuning the
> question
> > at hand?
> >
> > Mark
> >
> > On Thu., 6 Dec. 2018, 21:09 Alex <nedomacho at gmail.com wrote:
> >
> >> More specifically, electrostatics. For the stuff I'm talking about, the
> >> LJ portion contributes ~20% at the most. When the change in energetics
> >> is a statistically persistent value of order kT (of which about 20%
> >> comes from LJ), the quantity of interest (~exp(E/kT)) changes by a
> >> factor of 2.72. Again, this is a fairly special case, but I can easily
> >> envision someone doing ion permeation across KcsA and the currents would
> >> be similarly affected. For instance, when I set all cutoffs at 1.0 nm,
> >> mdrun ends up using something like 1.1 nm for electrostatics, at least
> >> that's what I see at the top of the log.
> >>
> >> I agree with what you said about vdW and it can be totally arbitraty and
> >> then often requires crutches elsewhere, but my question was whether for
> >> very sensitive quantities mdrun ends up utilizing the forcefield as it
> >> was designed and not in a "slightly off" regime. Basically, you asked me
> >> to describe our case and why I think there may be a slight issue, so
> >> there it is.
> >>
> >> Alex
> >>
> >> On 12/5/2018 10:34 PM, Mark Abraham wrote:
> >>> Hi,
> >>>
> >>> One needs to be more specific than NB. There is evidence that VDW
> cutoffs
> >>> of traditional lengths cause approximation errors that cause
> compensating
> >>> parameterization errors elsewhere; those effects get worse if the
> system
> >> is
> >>> inhomogeneous. Accordingly, mdrun never touches VDW cutoffs.
> >> Electrostatic
> >>> with PME is quite another matter - there you need sufficient overall
> >>> accuracy, and there are multiple equivalent ways to do that.
> >>>
> >>> Mark
> >>>
> >>>
> >>> On Thu., 6 Dec. 2018, 09:56 Alex <nedomacho at gmail.com wrote:
> >>>
> >>>> Hi Mark,
> >>>>
> >>>> I am not sure it is a concern, to be honest, so let me just lay out my
> >>>> thoughts and maybe you could share your opinion.
> >>>>
> >>>> I recently shared a link for our recent paper
> >>>> (https://www.nature.com/articles/s41563-018-0220-4), in which the
> >>>> quantity of interest is ion current via pores that disallow what we
> >>>> normally mean by diffusive permeation. Instead, there are considerable
> >>>> barriers and ionic currents are rather precisely described by
> >>>> exp(-E/kT), where E is some energy calculated from nonbonded
> >>>> interactions and includes a huge contribution from the solvent. It is
> my
> >>>> understanding that NB stuff gets parameterized at a particular cutoff
> >>>> value and our results are rather sensitive to that. I can't say we're
> >>>> dying to have extreme repeatability, but is it in your opinion
> >>>> acceptable to have variability in the cutoff radii and the rlist
> between
> >>>> something like 1.0 - 1.2 nm? To begin with, I am not particularly
> >>>> worried about it, because we mostly report on qualitative behaviors,
> but
> >>>> I am interested in your opinion. I have read the manual and
> >>>> unfortunately there is nothing in the way of actually showing
> estimates
> >>>> of NB energy variation as a function of small differences in cutoffs.
> >>>>
> >>>> Thank you,
> >>>>
> >>>> Alex
> >>>>
> >>>>
> >>>> On 12/5/2018 3:36 PM, Mark Abraham wrote:
> >>>>> Hi,
> >>>>>
> >>>>> There's quite detailed discussion of the treatment of pair searching
> in
> >>>>> section 3.4.2 of the reference manual. Perhaps that clarifies things?
> >>>> We're
> >>>>> not aware of a reason to want to control things manually, but if you
> >> have
> >>>>> one, we're keen to hear of it!
> >>>>>
> >>>>> Mark
> >>>>>
> >>>>>
> >>>>> On Wed., 5 Dec. 2018, 09:59 Alex <nedomacho at gmail.com wrote:
> >>>>>
> >>>>>> Hi all,
> >>>>>>
> >>>>>> We've long noticed that at the beginning of simulations mdrun goes
> >>>> through
> >>>>>> what seems like trying to adjust the short-range NB radii to its
> >> liking.
> >>>>>> What is up with that and does this mean that every simulation
> proceeds
> >>>> with
> >>>>>> a new cutoff? If so, is there a way to disable this?
> >>>>>>
> >>>>>> Thank you,
> >>>>>>
> >>>>>> Alex
> >>>>>> --
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