Using BAT Internal Coordinates

lauren finn

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Nov 22, 2021, 10:14:03 AM11/22/21

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Hello!

I've managed to calculate the configurational entropy for some dipeptides using cartesian coordinates. However, I would like to do the same calculation using internal BAT coordinates.

I see the module 4.2.7. Bond-Angle-Torsion coordinates analysis — MDAnalysis.analysis.bat  and I am able to convert the trajectory and get an estimate under the new coordinate system. But I can't tell which bond / angle / torsion is referenced under each coordinate. The attribute "results.bat" explains the first 6 coordinates are the external degrees of freedom and "...the rest of the array consists of all the other bond distances, all the other bond angles, and then all the other torsion angles." But what specific internal coordinate is referenced in each column? Is there a way to determine this?

Best,

Lauren

Oliver Beckstein

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Nov 22, 2021, 11:58:10 AM11/22/21

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Hi Lauren,

Welcome to the MDAnalysis list!

I don’t have experience with the BAT module and I agree with you that you’re asking a very sensible question.

Looking at the code https://github.com/MDAnalysis/mdanalysis/blob/735abb8c76d71e1dc8197d73ee6f5d1845634914/package/MDAnalysis/analysis/bat.py#L405-L417 where the bonds are between _ag1 and _ag2, angles between _ag1, _ag2, and _ag3, and torsions _ag1, _ag2, _ag3, _ag4 it looks that everything is based on the “torsions list”, which is found in _torsions. I think your best bet (short of someone answering your question directly) is to look into _agX .

The Cartesian() method has code to “conveniently split the BAT vector into new variables” at https://github.com/MDAnalysis/mdanalysis/blob/735abb8c76d71e1dc8197d73ee6f5d1845634914/package/MDAnalysis/analysis/bat.py#L495-L502 , which might help you with properly associating an internal coordinate with a pair, triplet, or quadruplet of atoms.

Oliver

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Oliver Beckstein (he/his/him)

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lauren finn

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Nov 24, 2021, 6:39:56 AM11/24/21

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Hi Oliver,

Thanks to your pointers, I see now how I can associate the internal coordinates to the atoms given in the torsions and root atoms. In my case, I used:

from MDAnalysis.analysis.bat import BAT

bat = BAT(selected_residues)

bat.run()

torsions = bat._torsions

root = bat._root

which gives a list AtomGroups containing 4 atoms, and an AtomGroup containing 3 atoms. So now I'm working on implementing an association between coordinate and atom indicies.