[gmx-users] mdrun-adjusted cutoffs?!

Discussion:

Alex

2018-12-04 22:35:17 UTC

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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Mark Abraham

2018-12-05 22:36:36 UTC

Permalink

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

Post by Alex
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
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or

Alex

2018-12-05 22:56:19 UTC

Permalink

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

Post by Mark Abraham
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

Mark Abraham

2018-12-06 05:34:51 UTC

Permalink

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

Post by Alex
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

Post by Mark Abraham
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

Post by Mark Abraham
not aware of a reason to want to control things manually, but if you have
one, we're keen to hear of it!
Mark

Post by Alex
Hi all,
We've long noticed that at the beginning of simulations mdrun goes

through