[gmx-users] kinetically trapped in a local minimum???

[Mark Abraham]

#NGUYEN CONG TRI# wrote:
> Dear Gromacs users,
>  
> How can we know that the system is properly equilibrated or whether we 
> should extend the equilibration step. Someone suggest that we look at 
> the potential energy to see whether it has converged? Is it correct?

That's one test. You should look for converged behaviour in a range of 
simulation observables that hopefully include those that will indicate 
that the observable(s) on which you plan to collect data in the 
production run are/will be showing equilibrated behaviour.

> One more question, normally, we carry out the equilibration at 300K, 
> don't we? 

If you're interested in a room-temperature system, that would be a 
logical choice. If you're interested in another temperature, be aware 
that most force fields are not parametrized on data from other temperatures.

> How can we know that this temperature is enough and the system 
> is not kinetically trapped in a local minimum? And if it is whether it 
> affects the production run later on? 

You can't ever tell from a single simulation in isolation. You can try a 
cheaper simulation at a higher-temperature or coarser-graining to get an 
idea how big the system space might be, or do simulated annealing (or 
other such nonlocal-search approaches), but there's never a guarantee 
that these reflect what's accessible in a dynamical system. An 
implicit-solvent replica-exchange MD simulation (e.g. with AMBER) can be 
instructive. Experience with similar systems can be a guide also.

Mark