We present a new approach for automated exploration of free energy landscapes on the basis of the umbrella integration (UI) method. The method to search points in the landscape relies on the normal distributions and gradients of the potential of mean force (PMF) obtained from UI calculations. We applied this approach to the alanine dipeptide in solution and demonstrated that the equilibrium and the transition states were efficiently found in the ascending order of the PMF values
Understanding how and why a protein folds to a well defined structure would be a great scientific ad...
The potential of mean force describing conformational changes of biomolecules is a central quantity ...
We have investigated the free energy surface of alanine tripeptide in water. To elucidate the second...
We present a new approach for automated exploration of free energy landscapes on the basis of the um...
The potential of mean force describing conformational changes of biomolecules is a central quantity ...
Many problems in biology, chemistry, and materials science require knowledge of saddle points on fre...
We present a method for determining the average transition path and the free energy along this path ...
A simple, efficient, and accurate method is proposed to map multidimensional free energy landscapes....
New algorithms for sampling and exploring multidimensional free energy surfaces(FES) are developed. ...
International audienceComputer simulations play an important role in the study of transformation pro...
The weighted histogram analysis method (WHAM) is a standard protocol for postprocessing the informat...
Computer simulations play an important role in the study of transformation processes of condensed ma...
A robust importance-sampling algorithm for mapping free-energy surfaces over geometrical variables, ...
<p>(A) Density of the data on the plane. There are six basins (a to f) in the density landscape. (B...
Umbrella sampling is an efficient method for the calculation of free energy changes of a system alon...
Understanding how and why a protein folds to a well defined structure would be a great scientific ad...
The potential of mean force describing conformational changes of biomolecules is a central quantity ...
We have investigated the free energy surface of alanine tripeptide in water. To elucidate the second...
We present a new approach for automated exploration of free energy landscapes on the basis of the um...
The potential of mean force describing conformational changes of biomolecules is a central quantity ...
Many problems in biology, chemistry, and materials science require knowledge of saddle points on fre...
We present a method for determining the average transition path and the free energy along this path ...
A simple, efficient, and accurate method is proposed to map multidimensional free energy landscapes....
New algorithms for sampling and exploring multidimensional free energy surfaces(FES) are developed. ...
International audienceComputer simulations play an important role in the study of transformation pro...
The weighted histogram analysis method (WHAM) is a standard protocol for postprocessing the informat...
Computer simulations play an important role in the study of transformation processes of condensed ma...
A robust importance-sampling algorithm for mapping free-energy surfaces over geometrical variables, ...
<p>(A) Density of the data on the plane. There are six basins (a to f) in the density landscape. (B...
Umbrella sampling is an efficient method for the calculation of free energy changes of a system alon...
Understanding how and why a protein folds to a well defined structure would be a great scientific ad...
The potential of mean force describing conformational changes of biomolecules is a central quantity ...
We have investigated the free energy surface of alanine tripeptide in water. To elucidate the second...