DCD Unit cell angles different between MDAnalysis and VMD #187
Description
Hello,
As discussed in the mailling list
(https://groups.google.com/forum/#!msg/mdnalysis-discussion/C5TbkZLB2Eo/vyzcafrF
1AkJ), alpha and gamma angles are swapped between VMD and MDAnalysis when
opening a DCD file (attached).
MDAnalysis
import MDAnalysis
u = MDAnalysis.Universe("sample.psf", "sample.dcd")
u.trajectory.ts.dimensions
array([ 38.42659378, 38.39310074, 44.75979996, 60.02891541, 90. , 90. ], dtype=float32)
VMD
vmd sample.psf sample.dcd
molinfo 0 get {a b c alpha beta gamma} (Using TkConsole)
38.426594 38.393101 44.759800 90.000000 90.000000 60.028915
The differences are caused by the indexing of the unitcell array when reading
DCD files. In lines 732, 734, 738 and 740 of dcd.c
(https://code.google.com/p/mdanalysis/source/browse/package/src/dcd/dcd.c#732),
MDAnalysis associates alpha to index 1, while gamma is set to index 4. When
looking at lines 01013, 01015, 01019 and 01021 of VMD's dcdplugin.c
(http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/dcdplugin_8c-source.html#l0
0947), the same indexes are swapped (4 for alpha and 1 for gamma).
This problem became apparent when dealing with a non-orthorhombic box, since
these exchanges make no difference for orthorhombic boxes.
Thanks
Original issue reported on code.google.com by caiobio...@gmail.com on 7 Jul 2014 at 4:44
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