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Molecular dynamics workflow directory structure
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NAMD-format cell basis vectors
I'd like analysis.tcl to be able to spit out NAMD-format cell basis vectors for inserting into sim_opt. This would take advantage of PBCTools in VMD.
Alignment before RMSF calculations.
In the a5 analysis script we should be aligning to some reference structure before doing RMSF calculations. Could do this using fitframes for every DCD file chunk.
bigdcd
I'd like to see the trajectory analysis taking advantage of bigdcd where possible...
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