MD-FEP simulations

The MD simulations were carried out under standard temperature and pressure. A 1 fs time step was used with SHAKE25 applied to bonds. A 2 fs time step with SHAKE was used in the d(IC)6 d(IC)6 —> d(GC)6 d(GC)6 calculations. The non-bonded interactions for DNA complexes were subject to 10 -12 A spherical cutoff whereas no cutoff was applied to solute-solute interactions to avoid cutoff artifacts on coulombic interactions between sodium ions with phosphates. In the case of d(IC)6 d(IC)6 —> d(GC)6 d(GC)6 calculations an 8 A spherical cutoff was applied to non-bonded interactions. A weak harmonic restraint of 5.0 kcal/mol was imposed to avoid the disruption of terminal base pairs during FEP simulations of netropsin —> 0 and 2-imidazole-distamycin —> distamycin calculations. 

M. Lauterbach G. Wipff, "Liquid-Liquid Extraction of Alkali Cations by Calix[4]crown lonophores Conformation and Solvent Dependent Na" " / Cs" " Binding Selectivity A MD FEP study in pure Chloroform and MD Simulations at the Water / Chloroform Interface" in Physical Supramolecular Chemistry 1996, L. Echegoyen A. Kaifer Ed. Kluwer Acad. Pub., Dordrecht pp 65-102. 

The free energy differences A qm/mm m) between different images along the path are calculated using MD simulations and the FEP theory [38],... 

Fig. 6.10. Comparison of overlap sampling and FEP calculation results for the free energy change along the mutation of an adenosine in aqueous solution (between A = 0.05 and 0.45) in a molecular dynamics simulation. The results represent the average behavior of 14 independent runs. (MD time step.) The sampling interval is 0.75 ps. The upper half of the plot presents the standard deviation of the mean (with gives statistical error) for AA as a function of sample size N the lower half of the plot gives the estimate of A A - for comparison of the accuracy, the correct value of AA is indicated by the bold horizontal line...

Among the methods discussed in this book, FEP is the most commonly used to carry out alchemical transformations described in Sect. 2.8 of Chap. 2. Probability distribution and TI methods, in conjunction with MD, are favored if there is an order parameter in the system, defined as a dynamical variable. Among these methods, ABF, derived in Chap. 4, appears to be nearly optimal. Its accuracy, however, has not been tested critically for systems that relax slowly along the degrees of freedom perpendicular to the order parameter. Adaptive histogram approaches, primarily used in Monte Carlo simulations - e.g., multicanonical, WL and, in particular, the transition matrix method - yield superior results in applications to phase transitions,... 

According to CASSCF (and nonhybrid functionals), the spin population on the Fe atom is close to 1.0, whereas the NO moiety does not carry a significant amount of spin density. Based on that, the Fe(I)-NO+ electronic structure was assigned to the FeP-NO complex. Earlier, (147) based on Car-Parinello MD simulations, the Fe(III)-NO electronic structure was suggested for the FeP-NO complex. Additional complications came from the comparison of N-0 bond length while the experimentally measured bond... 

Thermodynamic cycles are used in MD simulations for computing accurate relative free energies. Free energy perturbation (FEP) calculations simulate the conversion of one molecule into another similar one (81,82). By... 

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