GROMOS starts counting from "1" in topologies (and other places). However, sometimes atom indices are 0 indexed (for example functions that use mdtraj). We should make this more consistent before too many people use functions.
I think we should stick to GROMOS convention and start everywhere from "1".
@MTLehner ideas?
GROMOS starts counting from "1" in topologies (and other places). However, sometimes atom indices are 0 indexed (for example functions that use
mdtraj). We should make this more consistent before too many people use functions.I think we should stick to GROMOS convention and start everywhere from "1".
@MTLehner ideas?