Feature #2005
Full Correlation Analysis (FCA) as Trajectory Analysis Module
Description
Why¶
Full Correlation Analysis (FCA) aids resolve conformational substates and identify actual transition pathways, usually much more successfully so than Principal Components Analysis (PCA).
Algorithm¶
FCA of a trajectory follows the spirit of PCA in finding important modes of motion through an orthonormal coordinate transformation and subsequent sorting of basis vectors.
While the projection of the trajectory on the subspace spanned by any two PCA basis vectors is linearly uncorrelated, they usually share mutual information (think of a circle).
The flavour of FCA to implement here, minimizes mutual information in the total system as defined by the information entropy H, I=\sum H[x_i]-H[{x}].
It starts from an intial guess of Eigenvectors from a PCA, then iteratively minimizes Mutual Information by 2d-planes rotations of pairs of basis vectors.
Implementation¶
The algorithm described here has been implmented for gromacs3 by Oliver Lange and then ported to gromacs4.6 by Christian Blau.
It should fit perfectly the trajectoryanlysis framework
References¶
Lange, Oliver F., and Helmut Grubmüller. "Full correlation analysis of conformational protein dynamics." Proteins: Structure, Function, and Bioinformatics 70.4 (2008): 1294-1312.
[[http://www.mpibpc.mpg.de/9619680/g_fca_ver_1_3.tgz]]
[[http://www.mpibpc.mpg.de/9768579/g_fca_ver_2_0.tgz]]
Associated revisions
History
#1 Updated by Mark Abraham almost 4 years ago
- Target version changed from 2018 to future
not happening for 2017
#2 Updated by Gerrit Code Review Bot almost 3 years ago
Gerrit received a related DRAFT patchset '1' for Issue #2005.
Uploader: berenger bramas (berenger.eu@gmail.com)
Change-Id: gromacs~master~Id9f8a59a82d9ae2d0ec2a49a19de7363d13c9a44
Gerrit URL: https://gerrit.gromacs.org/7552
Start using MDLogger in gmxpreprocess
Changed logging of one set of routines to use the logger interface
instead of calling fprintf to stderr.
Refs #2005, #2999
Change-Id: Ibbecab0af6a0fa1c62c754f8826b8ff84fa4886e