search

graeter-group / kimmdy

Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)
https://graeter-group.github.io/kimmdy/
GNU General Public License v3.0
8 stars 1 forks source link

Overview relax structure after reaction #18

Closed ehhartmann closed 1 year ago

KRiedmiller commented 2 years ago

Equilibration can be done in different ways of varying complexity and applicability. Free energy pertubation is the most broadly usable method, but also quite complex, while performing a short MD with small timesteps would be the easiest to implement.

ehhartmann commented 2 years ago

This issue is about the nvt and npt equilibration before the equilibrium and pulling MD. We might want to specify all our kinds of equilibrations as we've already got equilbration and equilibrium MD and now the equilibration after reaction.

KRiedmiller commented 2 years ago

Sorry for hijacking, now its for keeping track of our progress with all variations of minimization and equilibration ;) nvt and npt equilibration was already in a earlier version or am I mistaken? Anyways, it should work given a correct config and mdps, only documentation and examples are missing.

ehhartmann commented 2 years ago

There might be some code left from Benedikt's implementation but we never ran a minimization and nvt, npt equilibration.