[gmx-users] mdrun-adjusted cutoffs?!

[Alex]

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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