Optimization angle problem. C-C and C-C-C-C

[ghutchis]

If you build C-C and add H, the H's are added in an eclipsed position (i.e. H-C-C-H angle is 0) but the lowest energy should be staggered (H-C-C-H angle 60). This is also not fixed in the geometry optimization. This also happens for larger molecules like C-C-C-C for some bonds.

Reported by: dcurtis3

[ghutchis]

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100 steps is simply not enough, if you repeat the "geometry optimization" a couple of times you get the staggered conformation. I'm working on a force field setup dialog to set the force field, number of steps, algorithm, etc.
For larger molecules the force field code (OB) has the SystematicRotorSearch which rotates the bonds and then selects the lowest energy conformation. I have added this function as an extra action in the ghemical extention.

Original comment by: @timvdm

[ghutchis]

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The other note to add to the bug report is that conjugate gradients is simply not efficient enough as an optimization mechanism. Now if Benoit adds matrix inversion to Eigen, then other optimization methods can be used in Open Babel.

I'm also working on a Monte Carlo conformer search, which would also be useful here.

-Geoff

Original comment by: @ghutchis

[ghutchis]

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BTW, I'm marking this "pending further comment." If Donald doesn't have any further comment, it will close in 14 days -- there's not really anything Avogadro can do, except wait for a better geometry optimization method in Open Babel.

-Geoff

Original comment by: @ghutchis

[ghutchis]

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This Tracker item was closed automatically by the system. It was
previously set to a Pending status, and the original submitter
did not respond within 14 days (the time period specified by
the administrator of this Tracker).

Original comment by: sf-robot