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

Xiaoliang Qian, Daniel Strahs, Tamar Schlick

Research output: Contribution to journalArticlepeer-review


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 languageEnglish (US)
Pages (from-to)1843-1850
Number of pages8
JournalJournal of Computational Chemistry
Issue number15
StatePublished - Nov 30 2001


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

ASJC Scopus subject areas

  • General Chemistry
  • Computational Mathematics


Dive into the research topics of 'A new program for optimizing periodic boundary models of solvated biomolecules (PBCAID)'. Together they form a unique fingerprint.

Cite this