[gmx-users] mdrun-adjusted cutoffs?!

Alex nedomacho at gmail.com
Sat Dec 8 21:45:28 CET 2018 

That's very valuable info, thank you.

By the way, all of our production mdp files have something like 
fourierspacing = 0.135, the origin of which is long gone from my memory. 
Does this imply that despite PME tuning our simulations use a fixed 
Fourier grid that ends up in suboptimal performance, or does the tuning 
override it?

Alex

On 12/8/2018 1:34 PM, Mark Abraham wrote:
> 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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