[gmx-users] mdrun-adjusted cutoffs?!

Alex nedomacho at gmail.com
Wed Dec 5 23:56:17 CET 2018

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? 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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