Superpositioning of flexible molecule ensembles: min(Var), min(Var+Prev), min(Var+NN)

Vytautas Gapsys, Bert L. de Groot
Optimal Superpositioning of Flexible Molecule Ensembles
Biophysical Journal, 2013, Vol. 104, Issue 1, pp. 196-207

The software contains three methods for superpositioning of flexible molecule ensembles by
a) minimizing variance, minVar
b) minimizing variance and distance to a previous frame
c) minimizing variance and RMSD in the local neighborhood

Usage:
-out: superpositioned ensemble
-log: variance over the trajectory after every iteration
-method: select one of the methods, described in detail in the publication
    1 - min(Var) minimizes variance over an ensemble
    2 - min(Var+Prev) minimizes variance and distance to a previous frame
    3 - min(Var+NN) minimizes variance and RMSD of the local neighborhood
-cycle_num: number of iterations
-NN: number of nearest neighbors to consider if method 3 is selected
-nt: number of threads to use for NN search if method 3 is selected
-nt_iter: number of threads to use for iterations. Be aware that
using more than one thread for -nt_iter option will superposition
molecules sligthly differently from a single threaded version

Download minVar