• 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
8.3.19 molLoad, modify, or delete a molecule in <strong>VMD</strong>. In the following, molecule number is a string describingwhich molecules are to be affected by the command. It is one of the following: all, top, active,inactive, displayed, on, off, fixed, free, or one of the unique integer ID codes assigned tothe molecules when they are loaded (starting with 0). The codes (molIDs) are not reused after amolecule is deleted, so if you, for example, have three molecules loaded (numbered 0, 1, 2), deletemolecule with molID equal to 0, and then load another molecule, the new molecule will have molID3. Thus, the list of available molecule IDs becomes (1 2 3). The index of the molecule on thislist is, among many other things, accessible through the molinfo command [§8.3.21]. In the abovecase, for example, molecule that was loaded the last has molID equal to 3, however, it is the thirdon the list of molecules, so it has the index equal to 2 (since we start countin from 0).The molecule representations (views) are assigned integer number (starting with 0 for eachmolecule), which appear in the list on the Graphics form [§4.4.7]. The representations can be added,deleted or changed with the mol command. See also sections on molinfo command [§ 8.3.21] formore ways of retrieving information about the representations.• new [ filename ][options ]:• addfile < filename >[options ]:mol new is used to create a new molecule from a file; if the optional filename parameteris omitted, a plain, “blank” molecule is created with no atoms (this can be used to createa canvas for drawing user-defined geometry). mol addfile is like mol new except that thestructure and coordinate data are loaded into the top molecule (whichever molecule was loadedlast) instead of creating a new one. Both mol new and mol addfile accept the following setof options:– type : Specifies the file type (psf, pdb, etc.) If this option is omitted, the filenameextension is used to guess the filetype; otherwise, it overrides what would be guessedfrom the filename.– first :– last :– step : For files containing coordinate frames , specifies which frames to load.Frames are indexed starting at 0. A step of 1 means all frames in the range will beloaded; a step of 2 means load every other frame.– waitfor : For files containing coordinate frames , specifies how many framesto load before returning; the default is 1. If frames is less than the number of framesin the file, the rest of the frames will be loaded in the background on subsequent <strong>VMD</strong>display updates. If frames is -1 or all, then all frames in all files still in progresswill be loaded at once before the command returns. Frames loaded this way will loadfaster than if they are loaded in the background. If files are still being loaded in thebackground when the addfile command is issued, frames from the files in progress willbe loaded first.– volsets : For files containing volumetric data, specifies which data sets toload. should be a list of zero-based indices.107
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VMD User’s GuideVersion 1.8.6Apri
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4.4.4 Molecule File Browser Form .
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8.3.20 molecule . . . . . . . . . .
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List of Figures2.1 Sample VMD sessi
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Chapter 1IntroductionVMD is a molec
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1.4 AcknowledgmentsThe authors woul
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• TachyonThe Tachyon multiprocess
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Figure 2.1: Sample VMD session disp
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2.5 An Introduction to Atom Selecti
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selection: protein and (name CA or
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no coordinate information. It must
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Chapter 4User Interface ComponentsV
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• Center (hot key ’c’)This mo
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Hot Key Command Purposer, R mouse m
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Hot Key Command Purpose+,f,F animat
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information. Atoms shows the number
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Animation SpeedThe rate of playback
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can change the view of the scene, e
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4/3 SCRHEIGHTi.e. 8.0YViewer’sEye
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Hiding a rep. To hide a rep, double
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Periodic TabThe Periodic tab contro
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• Name - the name of the atom as
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Figure 4.10: The Material Formslide
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force-feedback (haptic) devices suc
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the simulated spring is connected t
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Figure 4.13: The Sequence formmolec
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vmd> set sel [atomselect top "water
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The decimal in ”1.0” is importa
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# get the sidechain atoms (CB and o
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Applying this to the alanin.pdb coo
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have the same number of atoms, then
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set transformation_matrix [measure
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}display update offfor {set i 0} {$
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Chapter 12Customizing VMD SessionsT
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• -nt : Do not display the VMD ti
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• VMDIMMERSADESKFLIP : Enable a s
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axes location lowerleftstage locati
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Index.mailcap, 177.vmdrc, 26, 89, 1
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VMDHTMLVIEWER, 174VMDIMAGEVIEWER, 1
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move, 35atom, 35fragment, 35highlig
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short circuit logic, 72, 75sleepcom