[gmx-users] mdrun-adjusted cutoffs?!

[Alex]

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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