Protein-specific coordinates based on index groups

Colvars / colvars

Collective variables library for molecular simulation and analysis programs

http://colvars.github.io/

GNU Lesser General Public License v3.0

196 stars 56 forks source link

Protein-specific coordinates based on index groups #666

Open jhenin opened 4 months ago

jhenin commented 4 months ago

The goal is to make the alpha_angles CVC (and dihedralPC) available on all back-ends.

TODO:

[x] allow for series of groups to describe non-contiguous alpha segments
[x] extend to dihedralPC
[ ] update documentation
[ ] regression & unit tests

giacomofiorin commented 3 months ago

A general comment: besides making those functions more portable there would be major advantages in making all CVCs rely on atom groups.

I think it would be great to just use the three groups groupCA, groupN and groupO consistently in all backends, and just have VMD and NAMD auto-fill them to preserve backward compatibility.

While working on #644 I realized that when that is done, CVCs that are based on centers of mass could easily be used any positions, including individual atoms. This would much simplify the data structures of the alpha and dihedPC.

jhenin commented 3 months ago

About making the groups groupCA, groupN and groupO generic: I realized that for the alpha CVC, we need to let the user specify several individual ranges of residues to track different alpha-helical segments. This is not compatible with having a single generic name for the index groups.

I don't get the comment about CVCs based on COMs being able to use individual atoms - isn't that already the case?