Using regexps in atom selections

[GiovanniBussi]

Since 68473e2ba3 we can use regexps in argument selection.

This could be extended to atom selection also. This, in combination with atom selections by name (#32) would allow for a very powerful selection syntax, e.g.: ATOMS=(ALA1:.) # the whole residue ATOMS=(.:CA) # all the C-alpha ATOMS=(.:(CA)|(CB)) # all the C-alpha and C-beta ATOMS=(.:H.) # all hydrogens ATOMS=(.:[^H].*) # all non-hydrogens

[OndrejMarsalek]

In Belfast, we spoke with Toni Giorgino about the possibility of calling either VMD or g_select directly from PLUMED input, in a way similar to what he does in his VMD plugin. This would be done only once during setup, as the reference structure does not change. In principle, those selection language can "react" to geometry changes, but I don't see a way to reasonably make use of that on the fly.

[GiovanniBussi]

I think it is a good idea. Probably the simplest way is to provide a command line tool in gromacs that preprocess the input file. When running on simple machines that could be done on the fly when plumed starts. On supercomputers, if using calls such as "system" is difficult, one could just preprocess the input in advance to produce a ready-to-use plumed.dat file.

[GiovanniBussi]

I think nobody is going to do this, so I mark this issue as closed