Calculations of relative free energy surfaces in configuration space using an integration method
โ Scribed by Cun Xin Wang; Hai Yan Liu; Yun Yu Shi; Fu Hua Huang
- Publisher
- Elsevier Science
- Year
- 1991
- Tongue
- English
- Weight
- 359 KB
- Volume
- 179
- Category
- Article
- ISSN
- 0009-2614
No coin nor oath required. For personal study only.
โฆ Synopsis
An integration method is presented for calculating, in conjuction with molecular dynamics, free energy differences between states separated in configuration space. A simple model system for liquid neon is used to illustrate the method. The potential of mean force for conformation change is evaluated and the results are in good agreement with that obtained from a direct calibration simulation
๐ SIMILAR VOLUMES
An improved method for the calculation of excess free energies of surface solutions is proposed. It is shown that, although the method is based on rigorous thermodynamic arguments, it is not free from nonthermodynamic parameters, which, as in the previous ones, may affect considerably the calculated
## Abstract The free energy perturbation (FEP) methodology is the most accurate means of estimating relative binding affinities between inhibitors and protein variants. In this article, the importance of hydrophobic and hydrophilic residues to the binding of adenosine monophosphate (AMP) to the fru
We use the resolution of the identity (RI ) as a convenient way to replace the use of four-index two-electron integrals with linear combinations of three-index integrals. The method is broadly applicable to a wide range of problems in quantum chemistry. We demonstrate the effectiveness of RI for the