[gmx-users] gmx cluster without allowing Z-rotation?

Christopher Neale chris.neale at alum.utoronto.ca
Tue Feb 28 22:26:51 CET 2017

Dear users:

does anybody know if a simple code modification will permit gmx cluster to do the fitting while allowing translation in X, Y, and Z but rotation only in X and Y? I'm trying to do structural clustering on a membrane protein where tilt may be an important feature so I don't want to cluster conformations with different tilts. I initially tried gmx trjconv proprocessing, first with translation, then with transxy+rotxy before gmx cluster, but I realized this won't work because it's a static fit to a single reference structure whereas clustering requires fitting for each pair of conformations separately.

I'm guessing that changing the call to do_fit() in gmx_cluster.c to do_fit_ndim(2,...) after an initial trjconv centering without rotation might work ???

Thank you,

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