VMD User's Guide

of periodic boundary conditions can be turned on. With the selupdate flag enabled, bothatom selections are updated as each frame is processed, allowing productive use of ”within”selections. The size of the unitcell has to be stored in the trajectory file or has to be setmanually for all frames with the molinfo command. The command uses by default only thecurrent active frame for both selections. Using an explicite frame range via first, last, andstep is recommended for most cases.• hbonds cutoff angle selection1 [selection2]: Find all hydrogen bonds in the given selection(s),using simple geometric criteria. Donor and acceptor must be within the cutoff distance, andthe angle formed by the donor, hydrogen, and acceptor must be less than angle from 180degrees. Only non-hydrogen atoms are considered in either selection. If both selection1 andselection2 are given, the selection1 is considered the donor and selection2 is considered theacceptor. If only one selection is given, all non-hydrogen atoms in the selection are consideredas both donors and acceptors. The two selections must be from the same molecule. Thefunction returns three lists; each element in each list corresponds to one hydrogen bond. Thefirst list contains the indices of the donors, the second contains the indices of the acceptors,and the third contains the index of the hydrogen atom in the hydrogen bond.Known Issue: The output of hbonds cannot be considered 100% accurate if the donor andacceptor selection share a common set of atoms.• inverse matrix: Returns the inverse of the given 4x4 matrix.• minmax selection: Returns two vectors, the first containing the minimum x, y, andz coordinatesof all atoms in selection, and the second containing the corresponding maxima.• rgyr selection [weight weight]: Returns the radius of gyration of atoms in selection usingthe given weight. The radius of gyration is computed as( n) (rgyr 2 ∑n)= w(i)(r(i) − ¯r) 2 ∑/ w(i)(8.1)i=1i=1where r(i) is the position of the ith atom and ¯r is the weighted center as computer by measurecenter.• rmsf selection [first first] [last last] [step step]: Returns the root mean square positionfluctuation for each selected atom in the selected frames. If no first, last, or step values areprovided the calculation will be done for all frames.• rmsd selection1 selection2 [weight weight]: Returns the root mean square distance betweencorresponding atoms in the two selections, weighted by the given weight. selection1 andselection2 must contain the same number of atoms (the selections may be from differentmolecules that have different numbers of atoms).• sasa srad selection [-points varname] [-restrictrestrictedsel] [-samplesnumsamples]: Returnsthe solvent-accessible surface area of atoms in the selection using the assigned radiusfor each atom, extending each radius by srad to find the points on a sphere that are exposedto solvent. If the restrictedsel selection is used, only solvent-accessible points near that selectionwill be considered. The restrict option can be used to prevent internal protein voids orpockets from affecting the surface area results. The points option can be used to see where104