Hi All,
I have an equilibrated system containing a protein embedded in a lipid bilayer. I intend to study the protein's selectivity for different ions. To do that I produced several copies of the system, in each of them one sodium/chloride ion was replaced with a different ion (with similar charge).
Given that the original system was already equilibrated, how extensive a re-equilibration of these new systems should be?
It depends on where the ion is. If it is solvated and far from the protein, just 100 ps is enough. If it is very close to the protein or even coordinated by some residues, you need some more times for local relaxations. You should check the time-dependence of the distance or some observables and see whether they are in the equilibrated state, i.e. fluctuations around equilibrium values.
Thanks,
It is solvated and far from the protein. I assumed a short equilibration will do.
Cheers!
Hi,
Equilibration, in general, is a hard term to define. As previously stated a short equilibration may be good enough. However, just to be on the safe side please discord some initial part of the production run.
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