Entropy and free energy of a mobile protein loop in explicit water.

ABSTRACT: Estimation of the energy from a given Boltzmann sample is straightforward since one just has to average the contribution of the individual configurations. On the other hand, calculation of the absolute entropy, S (hence the absolute free energy F) is difficult because it depends on the entire (unknown) ensemble. We have developed a new method called "the hypothetical scanning molecular dynamics" (HSMD) for calculating the absolute S from a given sample (generated by any simulation technique). In other words, S (like the energy) is "written" on the sample configurations, where HSMD provides a prescription of how to "read" it. In practice, each sample conformation, i, is reconstructed with transition probabilities, and their product leads to the probability of i, hence to the entropy. HSMD i

SUBMITTER: Cheluvaraja S 

PROVIDER: S-EPMC2671085 | biostudies-literature | 2008 Aug

REPOSITORIES: biostudies-literature