Use of Molecular Dynamics for the Refinement of an Electrostatic Model for the In Silico Design of a Polymer Antidote for the Anticoagulant Fondaparinux

Figure 5

Free-energy profile (PMF) for the interaction of fondaparinux with R4-2 (𝑛 = 8). Calculated values are the Helmholtz free energy which approximates the Gibbs free energy for systems in the condensed phase [39, 40]. Simulations were performed using a step size of 0.5 Å and a simulation time of 60 ps at each interval. The error bars represent the 95% confidence intervals for 𝑛 number of replicates.