<div dir="ltr">Hi,<div><br></div><div>Thanks indeed for the report and concern. I echo Berk's observation that the numerical differences in forces between the trajectories in your tarball are within the expected range for different implementations of the same calculation.</div><div><br></div><div>mdrun -rerun velocities (and derived quantities) are disaster zone (see <a href="http://redmine.gromacs.org/issues/1868">http://redmine.gromacs.org/issues/1868</a>) and frankly I regard anything to do with them as wrong until proved correct. positions and forces should generally be OK, but despite the usefulness of rerun workflows, nobody has had time to care about my tests of this functionality at <a href="https://gerrit.gromacs.org/#/c/5435/">https://gerrit.gromacs.org/#/c/5435/</a> (though the multiple bugs they identified have been fixed). You will definitely get slightly different forces between mdrun and rerun if the original mdrun wrote positions and forces from a step that did not compute energies, because rerun always computes energies and when energies are computed the code paths that compute forces are generally different. I can't tell whether any of this has bearing on your observations with PLUMED, though, because I don't know what your calculation with it was doing.</div><div><br></div><div>Cheers,</div><div><br></div><div>Mark</div></div><br><div class="gmail_quote"><div dir="ltr">On Tue, May 17, 2016 at 9:59 AM Carlo Camilloni <<a href="mailto:carlo.camilloni@gmail.com">carlo.camilloni@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi<br>
<br>
The x must be identical because I used -rerun to parse the trr file, while<br>
I don’t know if the velocities are recalculated by rerun.<br>
What I am sure about is that the differences observed with metadynamics<br>
are highly significant.<br>
Right now I don’t have more time to investigate this, I will definitely<br>
do it as soon as I can, but if you have time i would have a further<br>
look into it..<br>
<br>
Cheers,<br>
Carlo<br>
<br>
<br>
> Message: 1<br>
> Date: Fri, 13 May 2016 12:10:52 +0200<br>
> From: Berk Hess <<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>><br>
> To: <a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a><br>
> Subject: Re: [gmx-developers] gromacs 2016 beta1 bug somewhere in the<br>
> new simd for bonded/LJ/lincs<br>
> Message-ID: <<a href="mailto:5735A82C.7080508@kth.se" target="_blank">5735A82C.7080508@kth.se</a>><br>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"<br>
><br>
> Hi,<br>
><br>
> In the files you sent I see that x and v are identical for all versions<br>
> and f has a few components that differ up to 0.002 kJ/mol/nm. This is<br>
> fully within the variation I would expect from different codes.<br>
> We need more evidence to judge if there is a bug present here. I can't<br>
> judge if the differences in your metadynamics results are significant<br>
> compared to the statistical accuracy.<br>
><br>
> Cheers,<br>
><br>
> Berk<br>
><br>
> On 2016-05-13 11:59, Carlo Camilloni wrote:<br>
>> Dear GMX developers,<br>
>><br>
>> First of all thanks for your continuos efforts in making gromacs better.<br>
>><br>
>> I have done a very basic calculation with the new gromacs-2016-beta1<br>
>> and I think there is a bug somewhere<br>
>> in the force calculation. (all calculations are run using 1 processor,<br>
>> no mpi, no openmp, no gpus)<br>
>><br>
>> I have run a calculation on alanine dipeptide:<br>
>><br>
>> 1) GMX507: 2 steps using 1 processor (avx2 simd and nothing else, the<br>
>> tpr is generated with gromacs 507)<br>
>> 2) rerun with GMX512 on the trr file<br>
>> 3) rerun with GMX2016 on the trr file<br>
>> and then I compared forces, velocities and energies, and while they<br>
>> are essentially the same for the step 0<br>
>> in the case of GMX507 and 512 they are not the same anymore for GMX2016b1.<br>
>><br>
>> The differences are not huge, even if from a rerun I would expect no<br>
>> differences at all, in particular on the<br>
>> forces, so I have run a metadynamics calculation from the same tpr<br>
>> file and using the three codes<br>
>> patched with plumed to see the effect on the free energy along the phi<br>
>> torsion angle, and unfortunately the<br>
>> difference is quite significant.<br>
>><br>
>> to be sure I repeated the same tests on a linux workstation (the first<br>
>> test was on my macbook), so different<br>
>> compilers and so on, but always avx2 simd)<br>
>><br>
>> here you can find everything (all the files I have generated):<br>
>> <a href="https://dl.dropboxusercontent.com/u/1349402/bug-report-aladip-2016.tgz" rel="noreferrer" target="_blank">https://dl.dropboxusercontent.com/u/1349402/bug-report-aladip-2016.tgz</a><br>
>><br>
>> I hope this helps.<br>
>><br>
>> Best,<br>
>> Carlo<br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
><br>
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