One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is irrelevant, however, if the absolute free energy of each state can be computed. We present a method for calculating the absolute free energy that employs a simple c...

Molecular dynamic (MD) simulations with both implicit and explicit solvent models have been carried out to study the folding dynamics of HP-36 protein. Starting from the extended conformation, the secondary structure of all three helices in HP-36 was formed in about 50 ns and remained stable in the remaining simulation. However, the formation of the tertiary structure was difficult. Although so...

Implicit solvent, coarse-grained models with pairwise interactions can access the largest length and time scales in molecular dynamics simulations, owing to absence of a huge number solvent particles, smaller interaction sites model molecules, lack fast sub-molecular degrees freedom. In this paper, we describe maximally for lipids implicit water. The is called ‘SiMPLISTIC’, which abbreviates ‘ ...

Efficient, accurate, and adaptable implicit solvent models remain a significant challenge in the field of molecular simulation. A recent model, IS-SPA, based on approximating mean force using superposition approximation, provides platform to achieve these goals. IS-SPA was originally developed handle non-polar solutes TIP3P water model but can be extended accurately treat polar other solvents. ...