### Abstract

An approach has been devised and tested for preserving the molecular dynamics molecular geometry taking into account energetic considerations during Reverse Monte Carlo (RMC) modeling. Instead of the commonly used fixed neighbor constraints, where molecules are held together by constraining distance ranges available for the specified atom pairs, here molecules are kept together via bond, angle, and dihedral potential energies. The scaled total potential energy contributes to the measure of the goodness-of-fit, thus, the atoms can be prevented from drifting apart. In some of the calculations (Lennard-Jones and Coulombic) nonbonding potentials were also applied. The algorithm was successfully tested for the X-ray structure factor-based structure study of liquid dimethyl trisulfide, for which material now significantly more sensible results have been obtained than during previous attempts via any earlier version of RMC modeling. It is envisaged that structural modeling of a large class of materials, primarily liquids and amorphous solids containing molecules of up to about 100 atoms, will make use of the new code in the near future.

Original language | English |
---|---|

Pages (from-to) | 2285-2291 |

Number of pages | 7 |

Journal | Journal of Computational Chemistry |

Volume | 33 |

Issue number | 29 |

DOIs | |

Publication status | Published - Nov 5 2012 |

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### Keywords

- computer modeling
- liquid structure
- molecular liquids
- Reverse Monte Carlo

### ASJC Scopus subject areas

- Chemistry(all)
- Computational Mathematics

### Cite this

**RMC-POT : A computer code for reverse monte carlo modeling the structure of disordered systems containing molecules of arbitrary complexity.** / Gereben, Orsolya; Pusztai, L.

Research output: Contribution to journal › Article

*Journal of Computational Chemistry*, vol. 33, no. 29, pp. 2285-2291. https://doi.org/10.1002/jcc.23058

}

TY - JOUR

T1 - RMC-POT

T2 - A computer code for reverse monte carlo modeling the structure of disordered systems containing molecules of arbitrary complexity

AU - Gereben, Orsolya

AU - Pusztai, L.

PY - 2012/11/5

Y1 - 2012/11/5

N2 - An approach has been devised and tested for preserving the molecular dynamics molecular geometry taking into account energetic considerations during Reverse Monte Carlo (RMC) modeling. Instead of the commonly used fixed neighbor constraints, where molecules are held together by constraining distance ranges available for the specified atom pairs, here molecules are kept together via bond, angle, and dihedral potential energies. The scaled total potential energy contributes to the measure of the goodness-of-fit, thus, the atoms can be prevented from drifting apart. In some of the calculations (Lennard-Jones and Coulombic) nonbonding potentials were also applied. The algorithm was successfully tested for the X-ray structure factor-based structure study of liquid dimethyl trisulfide, for which material now significantly more sensible results have been obtained than during previous attempts via any earlier version of RMC modeling. It is envisaged that structural modeling of a large class of materials, primarily liquids and amorphous solids containing molecules of up to about 100 atoms, will make use of the new code in the near future.

AB - An approach has been devised and tested for preserving the molecular dynamics molecular geometry taking into account energetic considerations during Reverse Monte Carlo (RMC) modeling. Instead of the commonly used fixed neighbor constraints, where molecules are held together by constraining distance ranges available for the specified atom pairs, here molecules are kept together via bond, angle, and dihedral potential energies. The scaled total potential energy contributes to the measure of the goodness-of-fit, thus, the atoms can be prevented from drifting apart. In some of the calculations (Lennard-Jones and Coulombic) nonbonding potentials were also applied. The algorithm was successfully tested for the X-ray structure factor-based structure study of liquid dimethyl trisulfide, for which material now significantly more sensible results have been obtained than during previous attempts via any earlier version of RMC modeling. It is envisaged that structural modeling of a large class of materials, primarily liquids and amorphous solids containing molecules of up to about 100 atoms, will make use of the new code in the near future.

KW - computer modeling

KW - liquid structure

KW - molecular liquids

KW - Reverse Monte Carlo

UR - http://www.scopus.com/inward/record.url?scp=84867071285&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84867071285&partnerID=8YFLogxK

U2 - 10.1002/jcc.23058

DO - 10.1002/jcc.23058

M3 - Article

VL - 33

SP - 2285

EP - 2291

JO - Journal of Computational Chemistry

JF - Journal of Computational Chemistry

SN - 0192-8651

IS - 29

ER -