Potential mean force calculations

Chipot, C. Kollman, P. A. Pearlman, D. A., Alternative approaches to potential of mean force calculations free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions, J. Comput. Chem. 1996,17, 1112-1131... 

Hartsough, D. S. and Merz Jr., K. M. Potential of mean force calculations on the SN1 fragmentation of tert-butyl chloride, J.Phys. Chem., 99 (1995), 384-390... 

The potential mean force (PMF) calculations by using the QM/MM-MD method has been used to obtain free energy change along the reaction coordinate in solution.138 141 TS optimization and minimum energy path calculations on the PES were carried out for a methyl-transfer reaction in water, and PMF calculations along the path were used to obtain the free energy of activation of... 

Hartsough, D. and K. M. J. Merz (1995). Potential of Mean Force Calculation on the SN1 Fragmentation of tert-Butyl Chloride. J. Phvs. Chem. 99 384-390. 

B. Maigret, D. A. Pearfman, and P. A. Kollman, Molecular dynamics potential of mean force calculations a study of the toluene-ammonium ir-cation interactions, J. Am. Chem. Soc. 118, 2998 3005 (1996). (b) J. W. Caldwell, and P. A. Kollman, Cation-ir interactions nonadditive effects are critical in their accurate representation, J. Am. Chem. Soc. 117, 4177-4178 (1995). 

Table 1 Computed electrostatic free energies (kcal/mol) of transfer for the orotate group in water (w) and in the enzyme ODCase (p) from the gas phase (g). AAG is obtained from potentials of mean force calculations (Fig. 2) and relative free energies are given with respect to the reactant state energy...

FI. Resat, M. Mezei, and J. A. McCammon,/. Phys. Ghent., 100, 1426 (1996). Use of the Grand Canonical Ensemble in Potential of Mean Force Calculations. 

C. Chipot, P. A. Kollman, and D. A. Pearlman,/. Comput. Chem., 17,1112 (1996). Alternative Approaches to Potential of Mean Force Calculations Free Energy Perturbation Versus Thermodynamic Integration Case Study of Some Representative Nonpolar Interactions. 

Table 5 Potential of mean force calculations uncertainty in in units of kT from simulations in which macroion separations are sampled ...

Even within the approach based on Cartesian coordinates, more Gauss Hermite terms are required for each coordinate at shorter separations. Figure 7 compares the modified potential energy —ksTlnZj r) as calculated using 3-16 terms. Within the repulsive regime, using too few terms leads to oscillations about the potential of mean force calculated with more terms. The smaller the separation included, the more terms required. 

Marrone, Hartsough, and Merz described a similar calculation for determination of the partial charges in potential of mean force calculations of 18-crown-6 and K+ in methanol using the MNDO Hamiltonian. 8 However, in their work, only a single solvent structure was used to calculate the MEP of the crown ether without ensemble averaging. These procedures should be valuable for deriving partial charges in empirical potential functions in future studies. 

KLEIN - You utilize the primitive model and experimental bulk water dielectric constant to normalize your potential of mean force calculations. Would it not be more natural to use the value of the dielectric constant appropriate to your water model (TIP P) How could this affect your results ... 

More quantitative insights into the energetic features of interface crossing have been obtained by "PMF" (Potential of Mean Force) calculations corresponding to the departure of ions and of ionophores from the interface to the water and organic phases, respectively These free energy profiles fully support trends observed in the free MD simulations. 

Norberg, J., Nilsson, L. (1995). Potential of mean force calculations of the stacking-unstacking process in single-stranded deoxyribodinucleo-side monophosphates. Biophysical Journal, 69,... 

Such a free energy is called a potential of mean force. Average values of Fs can be computed in dynamics simulations (which sample a Boltzmann distribution), and the integral can be estimated from a series of calculations at several values of s. A third method computes the free energy for perturbing the system by a finite step in s, for example, from si to S2, with... 

M J1990. Calculation of Conformational Ensembles from Potentials of Mean Force. An Approach o the Knowledge-Based Prediction of Local Structures in Globular Proteins. Journal of Molecular Siology 213 859-883. 

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