[gmx-users] mdrun-adjusted cutoffs?!
mark.j.abraham at gmail.com
Thu Dec 6 07:07:37 CET 2018
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.
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,
> 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?
> > 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
> >> 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
> >> a new cutoff? If so, is there a way to disable this?
> >> Thank you,
> >> Alex
> >> --
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