search for: dihedral

Displaying 2 results from an estimated 2 matches for "dihedral".

2010 Mar 31
2
Generative Topographic Map
...W <- gtm_ri(T,FI) Y= FI%*%W b = gtm_bi(Y) lambda <- 0.001 for (m in 1:15) { trnResult = gtm_trn(T, FI, W, lambda, 1, b, 2,quiet = TRUE, minSing = 0.01) W = trnResult$W b = trnResult$beta Y = FI %*% W } I ran the above script on my own data representing 1969 samples of 7 dihedral angles of a folding molecule (attached. Upon running the 1st iteration of the training function "gtm_trn" I get the following error that I cannot interpret. Any help and/or suggestion is welcome: > trnResult = gtm_trn(T, FI, W, lambda, 1, b, 2,quiet = TRUE, minSing = 1.) Error in gtm...
2010 Mar 01
0
Is package "dr" appropriate for reducing the dimensionality of molecules conformational space ?
...eduction problems. Some scientists concerned with drug discovery performed several steered Molecular Dynamics simulations of the alanine-dipeptide molecule dragged by a radial force from an equilibrium conformation to another different equilibrium conformation. They sampled at regular intervals 7 dihedral angles, 5 bending angles, and 4 atom pair distances all along the trajectory from the initial to the final conformation. Likewise they also calculated the work done on the molecule by the applied force. When a real system is simulated (this is a toy model) macro-molecules conformational space is hu...