### Abstract

Simulations of solvated macromolecules often use periodic lattices to account for long-range electrostatics and to approximate the surface effects of bulk solvent. The large percentage of solvent molecules in such models (compared to macromolecular atoms) makes these procedures computationally expensive. The cost can be reduced by using periodic cells containing an optimized number of solvent molecules (subject to a minimal distance between the solute and the periodic images). We introduce an easy-to-use program "PBCAID" to initialize and optimize a periodic lattice specified as one of several known space-filling polyhedra. PBCAID reduces the volume of the periodic cell by finding the solute rotation that yields the smallest periodic cell dimensions. The algorithm examines rotations by using only a subset of surface atoms to measure solute/image distances, and by optimizing the distance between the solute and the periodic cell surface. Once the cell dimension is optimized, PBCAID incorporates a procedure for solvating the domain with water by filling the cell with a water lattice derived from an ice structure scaled to the bulk density of water. Results show that PBCAID can optimize system volumes by 20 to 70% and lead to computational savings in the nonbonded computations from reduced solvent sizes.

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

Pages (from-to) | 1843-1850 |

Number of pages | 8 |

Journal | Journal of Computational Chemistry |

Volume | 22 |

Issue number | 15 |

DOIs | |

State | Published - Nov 30 2001 |

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### Keywords

- Molecular dynamics
- Particle-mesh Ewald
- Periodic boundary conditions
- Solvation
- Space-filling polyhedra

### ASJC Scopus subject areas

- Chemistry(all)
- Safety, Risk, Reliability and Quality

### Cite this

*Journal of Computational Chemistry*,

*22*(15), 1843-1850. https://doi.org/10.1002/jcc.1135

**A new program for optimizing periodic boundary models of solvated biomolecules (PBCAID).** / Qian, X.; Strahs, D.; Schlick, Tamar.

Research output: Contribution to journal › Article

*Journal of Computational Chemistry*, vol. 22, no. 15, pp. 1843-1850. https://doi.org/10.1002/jcc.1135

}

TY - JOUR

T1 - A new program for optimizing periodic boundary models of solvated biomolecules (PBCAID)

AU - Qian, X.

AU - Strahs, D.

AU - Schlick, Tamar

PY - 2001/11/30

Y1 - 2001/11/30

N2 - Simulations of solvated macromolecules often use periodic lattices to account for long-range electrostatics and to approximate the surface effects of bulk solvent. The large percentage of solvent molecules in such models (compared to macromolecular atoms) makes these procedures computationally expensive. The cost can be reduced by using periodic cells containing an optimized number of solvent molecules (subject to a minimal distance between the solute and the periodic images). We introduce an easy-to-use program "PBCAID" to initialize and optimize a periodic lattice specified as one of several known space-filling polyhedra. PBCAID reduces the volume of the periodic cell by finding the solute rotation that yields the smallest periodic cell dimensions. The algorithm examines rotations by using only a subset of surface atoms to measure solute/image distances, and by optimizing the distance between the solute and the periodic cell surface. Once the cell dimension is optimized, PBCAID incorporates a procedure for solvating the domain with water by filling the cell with a water lattice derived from an ice structure scaled to the bulk density of water. Results show that PBCAID can optimize system volumes by 20 to 70% and lead to computational savings in the nonbonded computations from reduced solvent sizes.

AB - Simulations of solvated macromolecules often use periodic lattices to account for long-range electrostatics and to approximate the surface effects of bulk solvent. The large percentage of solvent molecules in such models (compared to macromolecular atoms) makes these procedures computationally expensive. The cost can be reduced by using periodic cells containing an optimized number of solvent molecules (subject to a minimal distance between the solute and the periodic images). We introduce an easy-to-use program "PBCAID" to initialize and optimize a periodic lattice specified as one of several known space-filling polyhedra. PBCAID reduces the volume of the periodic cell by finding the solute rotation that yields the smallest periodic cell dimensions. The algorithm examines rotations by using only a subset of surface atoms to measure solute/image distances, and by optimizing the distance between the solute and the periodic cell surface. Once the cell dimension is optimized, PBCAID incorporates a procedure for solvating the domain with water by filling the cell with a water lattice derived from an ice structure scaled to the bulk density of water. Results show that PBCAID can optimize system volumes by 20 to 70% and lead to computational savings in the nonbonded computations from reduced solvent sizes.

KW - Molecular dynamics

KW - Particle-mesh Ewald

KW - Periodic boundary conditions

KW - Solvation

KW - Space-filling polyhedra

UR - http://www.scopus.com/inward/record.url?scp=0035976324&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0035976324&partnerID=8YFLogxK

U2 - 10.1002/jcc.1135

DO - 10.1002/jcc.1135

M3 - Article

AN - SCOPUS:0035976324

VL - 22

SP - 1843

EP - 1850

JO - Journal of Computational Chemistry

JF - Journal of Computational Chemistry

SN - 0192-8651

IS - 15

ER -