Assists in determining an optimal unit cell for single structures and ensembles. SQUEEZE is a method that was developed for setting up molecular simulations with periodic boundary conditions. It starts out as a routine optimization of an existing algorithm to handle ensembles more efficiently. It results in new approaches to construct contact bodies and bodies of minimal distance, as well as a new method to determine the optimal packing from them.
Molecular Dynamics Group, Groningen Institute for Biotechnology and Biomolecular Sciences, University of Groningen, Groningen, The Netherlands; Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands; Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, Groningen, The Netherlands
SQUEEZE funding source(s)
Supported by the European Union FP6 STREP “BacAbs MS” (Grant Number: LSHB-CT- 2006-037325) and the European Union FP7 I3 project “eNMR” (contract number 213010-e-NMR).