Some practical aspects of free energy calculations from molecular dynamics simulation

✍ Scribed by Sen, Srikanta; Nilsson, Lennart

• Publisher: John Wiley and Sons
• Year: 1999
• Tongue: English
• Weight: 211 KB
• Volume: 20
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/(sici)1096-987x(199906)20:8<877::aid-jcc12>3.0.co;2-o

✦ Synopsis

In this work, we address two critical aspects of calculation of the free energy differences in molecular systems from molecular simulations. The first aspect involves checking whether the calculated free energy difference depends significantly on the extent of perturbation used for accomplishment of a given transformation. The second aspect of interest is to verify if the sampling errors in calculating the free energy differences between the wild-type molecule and a mutated one in its free state and in a complex are similar, or not, for a finite-length dynamic simulation. The reliability of the free energy estimates obtained from molecular simulations using thermodynamic cycles depends in part on this fact. For investigating these aspects, we use a self-transformation scheme in which a transformation of a part of a molecular system into itself is considered. We perform MD simulations of DNA fragments in which a part of a specific base is subjected to such a self-transformation. Results indicate that the estimated free energy differences do not depend significantly on the extent of perturbation used to achieve the transformation. Interestingly, the variation in the cumulative free energy difference, ⌬ A, with the coupling parameter, , depends significantly on the extent of perturbation. We examine the physical basis of the observed nature of the variation of the accumulated free energy difference, ⌬ A, against the value in the case of a self-transformation. In a thermodynamic cycle, the sampling errors due to the finite-length simulation for the molecular system are found to be similar to each other for the two Ž . perturbations free and in a complex justifying the use of such approach in calculating ⌬⌬ A in molecular complexes.