[gmx-users] mdrun-adjusted cutoffs?!

[Szilárd Páll]

BTW if you have doubts and still want to make sure that the mdrun PME
tuning does not affect your observables, you can always do a few runs
with a fixed rcoulomb > rvdw set in the mdp file (with -notunepme
passed on the command line for consistency) and compare what you get
with the rcoulomb = rvdw case. As Mark said, you should not observe a
difference.

--
Szilárd
On Fri, Dec 7, 2018 at 7:10 AM Alex <nedomacho at gmail.com> wrote:
>
> I think that answers my question, thanks. :)
>
> On 12/6/2018 9:38 PM, Mark Abraham wrote:
> > 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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