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...