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<div class="moz-cite-prefix">Hi,<br>
<br>
In the files you sent I see that x and v are identical for all
versions and f has a few components that differ up to 0.002
kJ/mol/nm. This is 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 judge if the differences in your metadynamics results are
significant compared to the statistical accuracy.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 2016-05-13 11:59, Carlo Camilloni wrote:<br>
</div>
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cite="mid:C8D2BFE2-E396-437E-AF6D-8CD41AB23669@gmail.com"
type="cite">
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Dear GMX developers,
<div class=""><br class="">
</div>
<div class="">First of all thanks for your continuos efforts in
making gromacs better.</div>
<div class=""><br class="">
</div>
<div class="">I have done a very basic calculation with the new
gromacs-2016-beta1 and I think there is a bug somewhere</div>
<div class="">in the force calculation. (all calculations are run
using 1 processor, no mpi, no openmp, no gpus)</div>
<div class=""><br class="">
</div>
<div class="">I have run a calculation on alanine dipeptide:</div>
<div class=""><br class="">
</div>
<div class="">1) GMX507: 2 steps using 1 processor (avx2 simd and
nothing else, the tpr is generated with gromacs 507)</div>
<div class="">2) rerun with GMX512 on the trr file</div>
<div class="">3) rerun with GMX2016 on the trr file</div>
<div class="">and then I compared forces, velocities and energies,
and while they are essentially the same for the step 0</div>
<div class="">in the case of GMX507 and 512 they are not the same
anymore for GMX2016b1.</div>
<div class=""><br class="">
</div>
<div class="">The differences are not huge, even if from a rerun I
would expect no differences at all, in particular on the</div>
<div class="">forces, so I have run a metadynamics calculation
from the same tpr file and using the three codes</div>
<div class="">patched with plumed to see the effect on the free
energy along the phi torsion angle, and unfortunately the </div>
<div class="">difference is quite significant.</div>
<div class=""><br class="">
</div>
<div class="">to be sure I repeated the same tests on a linux
workstation (the first test was on my macbook), so different</div>
<div class="">compilers and so on, but always avx2 simd)</div>
<div class=""><br class="">
</div>
<div class="">here you can find everything (all the files I have
generated):</div>
<div class=""><a moz-do-not-send="true"
href="https://dl.dropboxusercontent.com/u/1349402/bug-report-aladip-2016.tgz"
class="">https://dl.dropboxusercontent.com/u/1349402/bug-report-aladip-2016.tgz</a></div>
<div class=""><br class="">
</div>
<div class="">I hope this helps.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Carlo</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
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