Hello, dear Gromacs community!
I’ve developed a trajectory analysis module for Gromacs with x3DNA/DSSR functionality (you can check it here), but free and with molecular dynamics trajectory analysis support.
I’d like to hear your opinion: do you consider it useful/necessary (or would you simply want) to include it in the core Gromacs package? Do you need such functionality for nucleic acid analysis?
Perhaps you’re interested in some specific data:
- secondary structure
- hydrogen bond networks
- base-pairs
- rigid frames (with parameters) for nucleotides/base-pairs/dinucleotide steps
- other (loops, multiplets, minor motifs, g-quartets, pseudoknots, etc.)
Also would you like to have nice visualization options for the data?
My developed module can only be included if it’s genuinely useful for Gromacs users.
Waiting for your comments and suggestions!
I would be very happy to see such a module included. The protein-centric nature of the built-in analysis tools is very limiting and we should open things up to nucleic acid analysis to become easier.
1 Like
Thank you very much for your reply.
I think you’re absolutely right about the protein-focused nature of the trajectory analysis modules in Gromacs. Indeed, I believe my module could add a nice set of nucleic acid analysis options (if integrated into the Gromacs base kit). It would be great if this will end up helpful to somebody.
Could I ask you what functionality in my module would interest you most? Hydrogen bond networks, base pair detection, their stability, determining helix types, and sugar-phosphate backbone geometry? Perhaps you’d be interested in understanding the secondary structure of nucleic acids? Identifying pseudoknots and, potentially, eliminating them? Perhaps you just needed some pretty pictures for your pretty research papers?
I would be grateful for any feedback.
I would be most interested in base-pairing persistence, helicoidal parameters, and backbone geometries. The rest of the features would not be something I would use much.