VMD User's Guide

the area contributions are coming from, and then the restrict flag can be used to eliminateany unwanted contributions after visualizing them. The varname parameter can be used tocollect the points which are determined to be solvent-accessible.• sumweights selection weight weights: Returns the sum of the list of weights (or data fieldto use for the weights) for all of the atoms in the selection.• bond atom list [options]: Returns the distance of the two specified atoms. The atoms arespecified in form of a list of atom indexes. Unless you specify a certain molecule through’molid molecule number’ these indices refer to the current top molecule. If the atoms are indifferent molecules you can use the form {{atomid1 [molid1]} {atomid2 [molid2]} ... } whereyou can set the molecule ID for the individual atoms. Note that measure bond does not careabout the bond that are specified in a psf file or that are drawn in VMD it just returns thedistance! Similar things are true for measure angle, dihed and imprp.The following options can be specified:– molid : The default molecule to which an atom belongs unless amolecule number was explicitely specified for this atom in the atom list. Further, allframe specifications refer to this molecule. (Default is the current top molecule.)– frame : By default the value for the current frame will be returned but aspecific frame can be chosen through this option. One can also specify all or last insteadof a frame number in order to get a list of values for all frames or just the last framerespectively.– first : Use this option to specify the first frame of a frame range. (Default isthe current frame.)– last : Use this option to specify the last frame of a frame range. (Default isthe last frame of the molecule).In case you specified the molecule IDs in the atom list then all frames specifications will referto the current top molecule unless a default molecule was set using the ’molid’ option. Sincethe top molecule can be different from the molecules involved in the selected atoms, it isgenerally a good idea to specify a default molecule.Here are a few examples of usage:measure bond {3 5} – Returns the bond energy between atoms 3 and 5 of the current frameof the top molecule˙ measure bond {3 5} molid 1 frame all – Returns the bond energybetween atoms 3 and 5 of molecule 1 for all frames.measure bond {3 {5 1}} molid 0 first 7 – Returns the bond energy between atoms 3of molecule 0 and atom 5 of molecule 1. The value is computed for all frames between theseventh and the last frame of molecule 0.• angle atom list [options]: Returns the angle spanned by three atoms. Same input format asthe ’measure bond’ command.• dihed atom list [options]: Returns the dihedral angle defined by four atoms. Same inputformat as the ’measure bond’ command.• imprp atom list [options]: Returns the improper dihedral angle defined by four atoms. Sameinput format as the ’measure bond’ command.105