![]() Some pathways may be more efficient than others (sometimes by many orders of magnitude). Only after free energy estimates have converged can the underlying parameters and physical assumptions really be tested.įree energy is a function of state, so there are many possible choices of pathway for a thermodynamic cycle connecting the same two endpoints. Without convergence, agreement with experiment may be due only to fortuitous cancellation of error. ![]() The goal is to obtain that free energy with as little statistical error as possible - and not necessarily to match experiment. Given this particular set of parameters and physical assumptionstarting point, there exists a single right answer for a free energy calculation. 6 Final Guideline: Verify, Verify, Verify!įree energies calculated from molecular simulation are appealing, because, in principle, they are rigorously correct, given a particular set of parameters and physical assumptions.5.3 Guideline 3: Correct for possible artifacts resulting from periodicity.5.2 Guideline 2: Be careful and rigorous when calculating statistical uncertainties.5.1 Guideline 1: Use TI, BAR, or MBAR to calculate free energies.4.3 Guideline 3: Use sufficiently rigorous underlying simulation techniques.4.1 Guideline 1: Equilibrium methods are easier to use for beginners than nonequilibrium or mixed-ensemble methods. ![]() 4 Guidelines for carrying out free energy calculations.3.4 Guideline 4: Think about whether your intermediate states are likely to converge or not.3.3 Guideline 3: Use few insertions/deletions. ![]()
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