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<div class="moz-cite-prefix">Hi,<br>
<br>
In molecular dynamics it's rather likely that you hit corner
cases, so we pay a lot of attention to numerical issues when
writing and reviewing code. Therefore it is unlikely that there
are cases that can be improved, but you are welcome to look.<br>
<br>
It is good that you mention the sign in dihedral angle. The return
value is actually never used. The sign is only used to set the
sign of the angle, which switches at angle=0, so there is no
stability issue.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 10/28/2017 07:16 AM, Pavel Panchekha wrote:<br>
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cite="mid:CAE4=OQ-TbMZOHNx3Ozjh_FLM0mKUbZhw_D1MnHKPMJuN7DqpTA@mail.gmail.com"
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<div class="gmail_default" style="font-size:small">Hello,</div>
<div class="gmail_default" style="font-size:small"><br>
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<div class="gmail_default" style="font-size:small">I'm a student
at the University of Washington working on numerical accuracy,
and I've been looking into GROMACS as an example of a beloved
and important large numerical program. Browsing through the
code base, I was struck by the computation of the dihedral
angle in <u>bonded.c</u>, at line 1569 (in GROMACS 5.1.4).</div>
<div class="gmail_default" style="font-size:small"><br>
</div>
<div class="gmail_default" style="font-size:small">I wonder if
it is possible for the <u>sign</u> variable to get the wrong
value, if the input points are close to one another or have
some other reason to experience cancellation when doing the
cross product. I think this is fixable using an adaptive
algorithm. Could changing the sign of the angle computed by <u>dih_angle</u>
affect GROMACS's results?<br>
</div>
<div class="gmail_default" style="font-size:small"><br>
</div>
<div class="gmail_default" style="font-size:small">More broadly,
has anyone ever had numerical accuracy issues with GROMACS?
Would there be interest in reviewing a patch that improved the
accuracy (for edge case inputs) for the dihedral angle
computation?<br>
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<div class="m_3853295731210088818gmail_signature"
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<div dir="ltr">—Pavel Panchekha</div>
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