VMD User's Guide

• energy energy term atom list [parameters] [options]: Returns the specified energy term fora given set of atoms. The energy term must be one of bond, angle, dihed, imprp, vdwor elect where vdw stands for ’van der Waals’ and elect for electrostatic energy. The energyis computed based on the CHARMM force field functions, the given parameters and thecurrent coordinates. All options for the measure bond command work for measure energy,too. Thus, you can for instance request energies for a range of frames of a trajectory. Alsothe format of the atom list is the same. The following parameters can be specified:– k : force constant for bond, angle, dihed and imprp energies in kcal/mol/A 2 orkcal/mol/rad 2 respectively.– x0 : equilibrium value for bond length, angle, dihedral angles and improperdihedrals in Angstrom or degree.– kub : Urey-Bradley force constant for angles in kcal/mol/A 2 .– s0 : Urey-Bradley equilibrium distance for angles in Angstrom.– n : dihedral periodicity.– delta : dihedral phase shift in degree (usually 0.0 or 180.0).– rmin1 : VDW equilibrium distance for atom 1 in Angstrom.– rmin2 : VDW equilibrium distance for atom 2 in Angstrom.– eps1 : VDW energy well depth (epsilon) for atom 1 in kcal/mol.– eps2 : VDW energy well depth (epsilon) for atom 2 in kcal/mol.– q1 : charge for atom 1.– q2 : charge for atom 2.– cutoff : nonbonded cutoff distance.– switchdist : nonbonded switching distance.For all omitted parameters a default value of 0.0 is assumed. For the electrostatic energy thedefault charges are taken from the according atom based field of the molecule. If the cutoffis not set or zero then no cutoff function will be used.8.3.18 menuThe menu forms of the GUI Control or query the on-screen GUI menu forms.• list: Return a list of the available menus• menu name on: Turnamenuon.• menu name off: Turnamenuoff.• menu name status: Returnon if on, off if off.• menu name loc: Return the xylocation.• menu name move xy: Move a menu to the given (x, y) locationThe parameter menu name is one of the following menu names: color, display, files, graphics, labels,main, material, ramaplot. render, save, sequence, simulation, or tool.106