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Expanded Ensemble mode

Expanded ensemble (EE) mode can be used for calculations of solvation free energies by gradual removal or insertion of molecules in the system. The theory and computational details behind the expanded ensemble method are described in papers (J.Chem.Phys.96, 1776 (1992); Molec.Simulations , 18, 43 (1996); J.Chem.Phys.,108,227 (1998)). Implementation of the EE approach here differs from the cited above articles, in a way that interaction parameters of the choosen solute molecule with the rest of the system are scaled with the coupling parameter $\alpha$, $0 \le \alpha \le 1$ according the folowing rules:


    $\displaystyle \sigma = const$ (12)
    $\displaystyle \epsilon \to \alpha^{n1} \epsilon$  
    $\displaystyle q \to \alpha^{n2} q$  

The coupling parameter $\alpha$ assumes a number of fixed values between 0 and 1, where ``1'' corresponds to the solute molecule properly inserted in the solvent, while value ``0'' correspons to the fully eleminated solute (which then can be considered as an a gas phase). The program computes probability distribution over subensembles with different values of $\alpha$, from which the free energy deffirence can be obtained. Additional bias for transition probabilities between subensembles is given by the so-called balancing factors, which need to be tuned in order to provide reasonable homogenious distribution of probabilities over subensembles.

Note 1: Special care should be taken in MDEE simulations of molecules having zero Lennard-Jones potential for hydrogen atoms (like SPC or TIP3P water). Simulation may become unstable when repulsive potential between oxygens becoms weeker while electrostatic attraction between hydrogen and oxygen still present. It is advisable to prescribe some small Lennard-Jones potential to such hydrogens.

Note 2: It is always recommended to use option ``Cut_forces'' with threshold level 0.05 - 0.1 in the case of EE simulation to avoid ``collisions'' with ``almost deleted'' particles

The expanded ensemble is specified by the following keywords:


next up previous contents
Next: Path Integral mode Up: The main input file Previous: Startup   Contents
Alexander Lyubartsev 2010-01-07