### Abstract

Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms. More recently outstanding advancement in both implicit solvent models and in entropy calculations are making the goal of free energy estimation from end-point simulations more feasible than ever before. We review briefly the basic theory and discuss the advancements in light of practical applications.

Original language | English (US) |
---|---|

Article number | 11 |

Journal | Frontiers in Molecular Biosciences |

Volume | 5 |

Issue number | FEB |

DOIs | |

State | Published - Feb 8 2018 |

### Fingerprint

### Keywords

- Continuum solvent
- Enthalpy
- Entropy
- Free energy
- Implicit solvent
- MM/GBSA
- Molecular dynamics simulations

### ASJC Scopus subject areas

- Molecular Biology
- Biochemistry
- Biochemistry, Genetics and Molecular Biology (miscellaneous)

### Cite this

*Frontiers in Molecular Biosciences*,

*5*(FEB), [11]. https://doi.org/10.3389/fmolb.2018.00011

**Free energy, enthalpy and entropy from implicit solvent end-point simulations.** / Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro.

Research output: Contribution to journal › Article

*Frontiers in Molecular Biosciences*, vol. 5, no. FEB, 11. https://doi.org/10.3389/fmolb.2018.00011

}

TY - JOUR

T1 - Free energy, enthalpy and entropy from implicit solvent end-point simulations

AU - Fogolari, Federico

AU - Corazza, Alessandra

AU - Esposito, Gennaro

PY - 2018/2/8

Y1 - 2018/2/8

N2 - Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms. More recently outstanding advancement in both implicit solvent models and in entropy calculations are making the goal of free energy estimation from end-point simulations more feasible than ever before. We review briefly the basic theory and discuss the advancements in light of practical applications.

AB - Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms. More recently outstanding advancement in both implicit solvent models and in entropy calculations are making the goal of free energy estimation from end-point simulations more feasible than ever before. We review briefly the basic theory and discuss the advancements in light of practical applications.

KW - Continuum solvent

KW - Enthalpy

KW - Entropy

KW - Free energy

KW - Implicit solvent

KW - MM/GBSA

KW - Molecular dynamics simulations

UR - http://www.scopus.com/inward/record.url?scp=85042106875&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85042106875&partnerID=8YFLogxK

U2 - 10.3389/fmolb.2018.00011

DO - 10.3389/fmolb.2018.00011

M3 - Article

VL - 5

JO - Frontiers in Molecular Biosciences

JF - Frontiers in Molecular Biosciences

SN - 2296-889X

IS - FEB

M1 - 11

ER -