[gmx-users] mdrun-adjusted cutoffs?!
nedomacho at gmail.com
Thu Dec 6 11:08:58 CET 2018
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.
On 12/5/2018 10:34 PM, Mark Abraham wrote:
> 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:
>>> 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!
>>> 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,
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