Hydrophobicity of small alkane molecules (propane dimer) in solvents: a classical molecular dynamics study

Molecular Dynamics (MD) simulations of propane dimer in different solvents (water, acetonitrile and methanol) were performed by using CHARMM platform for modeling the solute and solvents. A series of Umbrella sampling MD simulations were carried out in each solvent separately and potential of mean force (PMFs) were calculated by using Weighted Histogram Analysis Method. Results show that two minima (contact minima and solvent separated minima) characterize the PMF of propane dimer in all three solvent environments. The contact minima are deeper and less sensitive to solvent environment for its position. However, significant effect in the position of second minima, solvent separated minima, was observed. Our study reveals that the interaction between propane dimer is softer in methanol and acetonitrile than in water. BIBECHANA 17 (2020) 1-12

“Crawling” on the self-assembly system: A molecular simulation of peptide position adjusting over self-assembly block

By combining non-equilibrium molecular dynamics(NEMD), umbrella sampling, and weighted histogram analysis method(WHAM), we calculated the potential of mean force of histidine peptide moving over a self-assembly structure. The reaction coordinate is along the main chain direction of the histidine peptide in the self-assembly structure. It is found that the energy needed for the histidine peptide with 3 and 5 residues while moving along the reaction coordinate is around -2.2 kCal/mol and -7.4 kCal/mol, respectively. And the histidine peptide crawls along the reaction coordinate, performing a snake-like movement. This result could illustrate how histidine peptide adjusts its position during self-assembly process.