scale 10rot left 0 0 -1 0 1 0 1 0 0device phantombuttons vrpnbuttons://odessa/Phantom0device phantomfeedback vrpnfeedback://odessa/Phantom0Using ToolsThere are several different “tools”, each of which can be used with any of the input devices 1 :• The Grab Tool mimics a pair of tweezers, and can be used to move molecules around onthe screen without any keyboard or mouse commands. Pressing a button connects the 3dcursor to the nearest molecule. Then, moving or rotating the tracker will cause the moleculeto move or rotate around on the screen.• The Rotate Tool is a tool for precisely rotating molecules with haptic devices. When abutton is pressed and released, the cursor is again connected to the molecule. With this tool,however, the center of the molecule is fixed, and the end of the haptic pointer is forced tolie on the surface of a sphere about this center. Moving the device around the surface ofthe sphere rotates the molecule, and another button click releases the molecule. There aredetentes — like the clicks commonly felt in a 2d dial — on the surface of the sphere, arrangedso that the user can rotate the molecule to precise 90-degree points. If the user holds downthe button for a while initially, he can feel the sphere and the detentes, but do not affect themolecule. This “preview mode” allows the user to find a good point from which to start therotation.• The Joystick Tool is the three-dimensional equivalent of a Joystick, for haptic devices.Pressing the button creates a virtual “spring,” holding the device to its current location. If itis pushed away from this point in some direction, the selected molecule starts sliding in thatdirection, with a velocity that is proportional to the displacement of the device. The joysticktool shows how a three dimensional input device can be used to supply relative (differential)coordinates instead of absolute coordinates.• The Tug Tool is a tool that allows interaction with running molecular dynamics simulations.Pressing the button connects the device with a simulated spring to the nearest atom, andpulling on it adds a force to the simulation. If a haptic device is being used, the user will feela force on his hand that is proportional to this force. In this way, the tug tool implementssomething like the click-and-drag that is commonly used with windowing systems.If an atom selection is assigned to the Tools, the the Tug Tool will apply a force to all theatoms in the selection. The force applied will be proportional to the masses of the atoms inthe selection, so that all atoms experience the same acceleration. When a Tool Selection hasbeen assigned, the Tug Tool will always affect that selection, even if the button is pressed farfrom any atoms in the selection; this is intended to make it easier for the user to apply forcesonly on those atoms he/she intends to steer.• The Spring Tool also allows interaction with running molecular dynamics simulations. Itworks like the Tug Tool except that when the button on the tracker is released near an atom,1 The tools have been designed to allow <strong>VMD</strong> to use haptic devices. Most of the tools can give force-feedback tothe user, but none of them require haptic devices in order to operate.50
the simulated spring is connected to it.modifying the list of active springs.See section 4.4.8 for information on viewing and• The Pinch Tool is similar to the Tug Tool, except that force is applied only along the axisdefined by the orientation of the tracker.• The Print Tool is meant to be used as a debugging aid when one first sets up <strong>VMD</strong> foruse with VRPN, the CAVE, or other 3-D input devices. When enabled, this tool prints textmessages to the <strong>VMD</strong> console indicating the current position of the tool in question. Thistool is useful when calibrating the various transformation matrices that operate on trackerposition and orientation data (whether in <strong>VMD</strong> or in VRPN, CAVElib, etc).To add a new tool to a <strong>VMD</strong> session, open the Tool form and click the Create Tool button. Thetool’s number and type are displayed in the list to the left. Devices can be added to the tool byselectingthemfromtheAdd Device menu, or removed with the Delete Device button. Some ofthe options that can be specified in the sensor configuration file can be edited in using the controlsbelow, and the tool’s type can be changed with the Type menu.4.4.13 Simulation Form<strong>VMD</strong> has the ability to work with a molecular dynamics program running on another computer,to interact with and display the results of a simulation as they are calculated. A major feature in<strong>VMD</strong> is the ability to add perturbative steering forces to a running simulation, which are incorporateddirectly into the dynamics calculation; we refer to this capability as Interactive MolecularDynamics (IMD). In order to run and IMD simulation it is necessary to have a molecular dynamicsprogram that supports the IMD communication protocol. To date, two such programs exist;NAMD, developed at University of Illinois, and Protomol, developed at Notre Dame. The restof the discussion in this chapter assumes you are using NAMD. See the NAMD home page 2 forinformation on obtaining NAMD.Interactive Molecular DynamicsIMD works by establishing a TCP connection between <strong>VMD</strong> and the molecular dynamics simulationprogram. NAMD, or whichever MD program is being used, acts as the server. In order toprepare NAMDto accept <strong>VMD</strong>’s IMD connection request, NAMDmust be configured to listen forincoming connections on a network port. Once NAMD has started up, may wait for the user toconnect through that port. When <strong>VMD</strong>connects to NAMDsuccesfully, the simulation commences.Before connecting to the remote simulation, the <strong>VMD</strong>user must first load a molecule correspondingto the system being simulated. The structure file should correspond to the same structure fileused by NAMD. Once the molecule is loaded and NAMD has been started and is listening for aconnection, you are ready to connect to the simulation and start receiving coordinates. To establisha connection, open the Sim form, enter the hostname on which NAMD is running and the porton which NAMD is listening for incoming connections, then press the Connect button to establishthe connection. If NAMD is running on several distributed nodes, <strong>VMD</strong> must connect to the rootnode on which NAMD initially started out.2 http://www.ks.uiuc.edu/Research/namd/51
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Sourceraster3dmsmsfaqbiocoretachyon
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version (2.2). Thus if you have Pyt
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9.6 High-level Python InterfaceVMD
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Chapter 11Molecular Analysis11.1 Us
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vmd> set sel [atomselect top "water
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set transformation_matrix [measure
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axes location lowerleftstage locati
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Index.mailcap, 177.vmdrc, 26, 89, 1
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short circuit logic, 72, 75sleepcom