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Article ID: 1239 - Last Modified: April 7, 2011

What are the major differences between the three Liaison sampling methods—Minimization, Hybrid Monte Carlo, and Molecular Dynamics—in terms of calculated results? Which one should I use?

Minimization sampling is by far the fastest, and normally recommended. Hybrid Monte Carlo sampling makes a short series of molecular dynamics steps, and then uses a standard Metropolis "Monte Carlo" test to decide whether to accept the new geometry or to go back and try again. This should be a very efficient sampling method. However, at this point we recommend using Molecular Dynamics as the more reliable of the two simulation (i.e., HMC and MD) methods for Liaison. We recommend that you use Minimization sampling as your default choice, but try Molecular Dynamics sampling if Minimization sampling does not yield good results, or if you just wish to see whether the results can be improved.

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