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 3
Free-energy profile (PMF) for the interaction of fondaparinux with (a) R1-1, ; (b) R3-1, ; (c) R4-1, ; and (d) R6-1, . 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 number of replicates.
