Hello Dan
Trying to wrap my head around this (Sorry :-) )
This makes sense, that is why there is a command to ignore imaging for RDF analyses. It should be, and is, done unless forced to not be done.
> One question - the .001 difference you mentioned for RDF was between
> image and noimage right? Not image and autoimage?
Well, analysing autoimaged trajectories and the “raw” unwrapped trajectories with the same rdf command, apparently including “image”, produces ever so slightly different results.
19.250000 1.000166 5.127417 | 19.250000 1.000167 5.127417
19.450000 0.999990 5.288961 | 19.450000 0.999989 5.288961
19.650000 1.000253 5.453882 | 19.650000 1.000254 5.453883
19.750000 1.000297 5.537602 | 19.750000 1.000295 5.537601
19.850000 1.000478 5.622186 | 19.850000 1.000480 5.622186
19.950000 0.999802 5.707567 | 19.950000 0.999801 5.707567
Though the autoimageing was done using an anchor and not just the default.
Summing up. For my purposes, regardless of if I’m analysing post production "autoimaged", production "wrapped" or unimagined trajectories, RDF and HBOND should both be run with the “in command” imaging turned on (default for RDF and by adding “image” for hbond”). This should not always be necessary both for most of the cases I am working with, it will likely be.
This also makes some sense performance wise as it seems that the autoimage command runs serial and not parallel.
Thank you and best regards
// Gustaf
> On 10 Nov 2020, at 15:19, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> There's a lot to unwrap here (forgive the pun) but I'll do my best to
> answer all of your questions.
>
> On Tue, Nov 10, 2020 at 6:13 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>>
>> 1) When would it be important to use the “noimage” option for radial analyses? I see the options though not the motivation and I have not been able to generate a difference larger than 0.001 with my trial sets
>
> Realistically, never. Not imaging the distances that go into the RDF
> in a system with PBC is not formally correct. The one difference you
> will notice here is calculation speed, since using the minimum image
> convention has a not insignificant cost associated with it. If you're
> doing something like a water oxygen RDF where you've got tons and tons
> of averaging, the differences will be slight. In cases where there are
> fewer entities to average over the differences will become more
> pronounced. So the keyword is there as a short-cut, but there's a
> reason imaging is always on when PBC are present.
>
> One question - the .001 difference you mentioned for RDF was between
> image and noimage right? Not image and autoimage?
>
>> 2) Is there any preference for using autoimage before performing hbond analysis or using the image option during the analysis.
>>
>
> So unlike the RDF, for the 'hbond' command' imaging of distances is
> *not* on by default. This is why you will see big differences between
> image/no imaging. Imaging is off because in many cases for 'hbond' to
> work right you don't really need it. If you're just looking at
> solute/solute hydrogen bonds for a single molecule, imaging is not
> needed. If you've done your imaging properly (e.g. via autoimage) in a
> well-solvated system so that there is a larger buffer of bulk water
> around your solute and no imaging artifacts exist, again imaging is
> not needed. However, if your system is more condensed you may indeed
> need imaging. So really it depends on your system.
>
>> Considering both efficiency and accuracy. Performing longer, large system simulations often produces large amounts of data. From an efficiency point of view, if there is a need to “autoimage” trajectories before analysing, the time consumption for this action and the extra disk space required may indicate using iwrap=1 during simulation being more efficient for these reasons.
>
> The problem here is that iwrap=1 does not image in a "smart" way - I
> think imaging is done based on the location of the first atom, so you
> can end up with imaging artifacts (like splitting DNA strands) - this
> was the whole reason 'autoimage' was even developed.
>
>> I have no idea regarding accuracy/performance hit of using the "noimage” option with radial so I donated know if this would outweigh the benefits.
>>
>> How would this compare to using iwrap=0 and image option in hbond with regard to speed/accuracy?
>
> Even if you image a trajectory before running hbond (or RDF for that
> matter), it's not the same as having imaging on in the command itself.
> As I said before, for 'hbond' it may _appear_ the same if none of your
> hydrogen bonds are across the periodic boundary, but otherwise image
> and noimage are two very different analysis modes.
>
>>
>> Is there potentially any nice overview indicating which analyses could be affected by wrapping and/or recommendations for settings not listed with the particular analyses in the manual?
>
> Not really, although this would probably be nice to add to the Actions
> table. In general if you search for 'image' in the cpptraj manual that
> will give you an idea:
> https://jenkins.jasonswails.com/job/amber-github/job/cpptraj/job/master/lastSuccessfulBuild/artifact/doc/CpptrajManual.pdf
>
> Hope this helps a bit,
>
> -Dan
>
>>
>> Best regards
>> // Gustaf
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Received on Wed Nov 11 2020 - 00:30:02 PST
