Paper Info
Title
A new program for optimizing periodic boundary models of solvated biomolecules (PBCAID).
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. (C) 2001 John Wiley & Sons, Inc.
Year
DOI
Venue
2001
10.1002/jcc.1135
JOURNAL OF COMPUTATIONAL CHEMISTRY
Keywords
Field
DocType
periodic boundary conditions,particle-mesh Ewald,molecular dynamics,space-filling polyhedra,solvation
Electrostatics,Mathematical optimization,Lattice (order),Computational chemistry,Polyhedron,Atom,Chemistry,Periodic boundary conditions,Solvation,Molecular dynamics,Periodic graph (geometry)
Journal
Volume
Issue
ISSN
22
15
0192-8651
Citations 
PageRank 
References 
1
0.47
1
Authors
3
Name
Order
Citations
PageRank
Xiaoliang Qian1875.18
Daniel Strahs271.67
Tamar Schlick325162.71