Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA.
Where this comes from
- Record sourced from PubMed, PMID 26192992.
- Also identified by DOI 10.1371/journal.pone.0131754 and PMC identifier 4507862.
- Licence recorded as CC0.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
We discuss recent advances of the VOTCA package for systematic coarse-graining. Two methods have been implemented, namely the downhill simplex optimization and the relative entropy minimization. We illustrate the new methods by coarse-graining SPC/E bulk water and more complex water-methanol mixture systems. The CG potentials obtained from both methods are then evaluated by comparing the pair distributions from the coarse-grained to the reference atomistic simulations. In addition to the newly implemented methods, we have also added a parallel analysis framework to improve the computational efficiency of the coarse-graining process.
Medical subject headings
- Algorithms
- Entropy
- Molecular Dynamics Simulation