Single-sweep methods for free energy calculations.
A simple, efficient, and accurate method is proposed to map multidimensional free energy landscapes. The method combines the temperature-accelerated molecular dynamics (TAMD) proposed in [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006)] with a variational reconstruction method using radial-basis functions for the representation of the free energy. TAMD is used to rapidly sweep through the important regions of the free energy landscape and to compute the gradient of the free energy locally at points in these regions. The variational method is then used to reconstruct the free energy globally from the mean force at these points. The algorithmic aspects of the single-sweep method are explained in detail, and the method is tested on simple examples and used to compute the free energy of the solvated alanine dipeptide in two and four dihedral angles.
Maragliano
Luca
L
Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA. maraglia@uchicago.edu
Vanden-Eijnden
Eric
E
D000409:Alanine / Q000737:chemistry*; D000465:Algorithms; D004151:Dipeptides / Q000737:chemistry*; D004735:Energy Transfer; D011487:Protein Conformation; D013816:Thermodynamics; D013997:Time Factors
D004151:Dipeptides; D000409:Alanine