#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
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