Fix/214

[fgrunewald]

No description provided.

[fgrunewald]

@ricalessandri this could be interesting for you. I've made a wrapper around gen_coords, called gen_replicas. It works in the same way and has the same arguments as gen_coords. However, you can give it a set of mdp files using '-mdp' flag. It will then use gmx wrapper - which you have to install beforehand - to execute gromacs simulations in order of the given mdp files. So if you provide min.mdp, NVT.mdp and prod.mdp it will run energy minization, NVT and then the production run in a separate directory. So basically now you can get the energy minization and equilibration in one go. Added bonus if you set the '-nrepl' flag you can generate multiple replica.

My idea was to combine this feature together with the automatic AA-ff generator. Because then you could to high throughput AA simulations quite easily.

Are there other features you think could be useful?

[ricalessandri]

hey @fgrunewald, cleaning up my old notes and found this back. Would this still work? I'd be interested in trying it out.

[fgrunewald]

In principle, it should. Someone would have to resolve the conflicts in bin/polyply. I think they just need to be copied from the current master.

I never liked the process runner though. Nowadays, I'd probably be able to design a better one around GromacsWrapepr