Hybrid clustering by using K-centers and K-medoidsĬalculate normal modes and anisotropic fluctuations by using Anisotropic Network Model.Ĭalculate normal modes of ANM using sparse-matrix for reducing memory sizeĬalculate normal modes of ANM for molecule with circular symmetry using symmetric coordinates Perform time-structure based Independent Component Analysis (tICA) Peform principal component analysis (PCA)
Multi-state Bennett Acceptrance Ratio Method (MBAR)Ĭalculate 1D potential of mean force from scattered 1D-data (using kernel density estimator)Ĭalculate 2D potential of mean force from scattered 2D-data (using kernel density estimator) Weighted Histogram Analysis method (WHAM) Statistics (WHAM, MBAR, clustering, etc) name Make a pairlist by searching pairs within a cutoff distanceĬalculate Q-score (fraction of native contacts) from given heavy atom coordinates Orient molecule using the principal axes of inertiaįinds all the atoms within cutoff distance from given atomsĬalculate distance from the Cartesian coordinates of two atomsĬalculate angle from the Cartesian coordinates of three atomsĬalculate dihedral angle from the Cartesian coordinates of four atoms Remove the center of mass from coordinates or velocities Geometry calculations (fitting of structures, distance, angles, dihedrals, etc) nameĬalculate average structure by iterative superimposing Write xplor or charmm (namd) format dcd file Read xplor or charmm (namd) format dcd file Read charmm or xplor type Protein Structure File (PSF) Write amber ascii-format trajectory format file Read amber ascii-format trajectory file including box size
php EGO_VIII Manual http : // de /~ heller / ego / manual / node93. edu / Research / vmd / plugins / molfile / dcdplugin.
# trj = readdcd ( 'ak.dcd' ) % See also writedcd % References for dcd format MolFile Plugin http : // uiuc. * filename - input dcd trajectory filename * index_atom - index or logical index for specifying atoms to be read * trj - trajectory * box - box size * header - structure variable, which has header information % Example Each row of 'trj' has the XYZ coordinates of atoms in order. # = readdcd ( filename, index_atom ) % Description The XYZ coordinates of atoms are read into 'trj' variable which has 'nstep' rows and '3*natom' columns. # trj = readdcd ( filename, index_atom ) help readpdb readdcd read xplor or charmm ( namd ) format dcd file % Syntax