[gmx-users] mdrun-adjusted cutoffs?!

Mark Abraham mark.j.abraham at gmail.com
Sat Dec 8 21:34:59 CET 2018 

Hi,

Note that that will compare runs of differently accurate electrostatic
approximation. For iso-accurate comparisons, one must also scale the
Fourier grid by the same factor (per the manual section on PME autotuning).
Of course, if you start from the smallest rcoulomb and use a fixed grid,
then the comparisons will be of increasing accuracy, which might be enough
for the desired conclusion.

Mark

On Sat., 8 Dec. 2018, 02:05 Szilárd Páll <pall.szilard at gmail.com wrote:

> 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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