TY - JOUR
T1 - Single-sweep methods for free energy calculations
AU - Maragliano, Luca
AU - Vanden-Eijnden, Eric
N1 - Funding Information:
We thank Giovanni Ciccotti and David Chandler for carefully reading the manuscript; Weinan E for pointing out sparse grid methods which prompted us to test our method in four dimensions; Ron Elber and Anthony West for their help with the MOIL code; Sara Bonella, Simone Meloni, Michele Monteferrante and Maddalena Venturoli for useful discussions; and finally, Eric Darve for suggesting the test using Eq. . This work was partially supported by NSF Grant Nos.DMS02-09959 and DMS02-39625, and by ONR Grant No.N00014-04-1-0565.
PY - 2008
Y1 - 2008
N2 - 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.
AB - 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.
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U2 - 10.1063/1.2907241
DO - 10.1063/1.2907241
M3 - Article
C2 - 18532802
AN - SCOPUS:43949084051
SN - 0021-9606
VL - 128
JO - Journal of Chemical Physics
JF - Journal of Chemical Physics
IS - 18
M1 - 184110
ER -