sbhakat
commented
2 years ago Hi Team Loos, Currently Plumed supports calling analysis packages such as MDAnalysis or MDtraj to design collective variables. One can call MDAnalysis as follows:
MOLINFO STRUCTURE=helix.pdb PYTHON_BIN=python
g1: GROUP ATOMS=@mda:backbonereplace @mda with @mdt for MDTraj
Two advantages of having a python wrapper for Plumed are: 1) on-the fly tracking of CVs during MD or enhanced sampling 2) ability to design complex collective variables which then can be used for different enhanced sampling algorithms.
Keeping in mind bigger community base of Plumed, popularity within enhanced sampling community and availability of several reweighting, analysis & enhanced sampling protocols, I believe a Loos integration with Plumed will be give both users a lot of flexibility.
In my experience loos does a lot of great job specially in terms of standard post-dynamics analysis but specially in case of membrane proteins. I think at this stage a Loos wrapper for Plumed is a natural choice which will bring a lot of synergy. Will be happy to discuss with Team Loos :)
agrossfield
mdt
maxbonomi
GiovanniBussi
Is your feature request related to a problem? Please describe. Not so much a problem as an expansion. Right now PLUMED often is used to perform analysis, and often it does this by calling tools or functions from within other analysis packages like MDAnalysis and MDTraj. It would be nice for loos to be an option for these users, as it would increase our user base and it would potentially be more performant than the alternatives. It's especially worthwhile if we can be included in some of PLUMED's extensive documentation, as many simulators come up referring to those docs.
Describe the solution you'd like Since I'm not a plumed user myself, I'm kind of the wrong guy to write this. Hoping other users who are more involved with PLUMED can add some detail here, but basically plumed script uses prefixes to indicate which surrogate library it ought to use, and what functionality should be called within that. It looks like a python wrapper.
Describe alternatives you've considered I just want LOOS everywhere I go. Is that too much to ask?
Additional context I got this suggestion from a fellow postdoc from the Bowman group, @sbhakat. I'll encourage him to comment on this to see if he has something more specific to request.