VMD User's Guide

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 VMD foruse with VRPN, the CAVE, or other 3-D input devices. When enabled, this tool prints textmessages to the VMD 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 VMD or in VRPN, CAVElib, etc).To add a new tool to a VMD 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 FormVMD 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 inVMD 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 VMD and the molecular dynamics simulationprogram. NAMD, or whichever MD program is being used, acts as the server. In order toprepare NAMDto accept VMD’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 VMDconnects to NAMDsuccesfully, the simulation commences.Before connecting to the remote simulation, the VMDuser 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, VMD must connect to the rootnode on which NAMD initially started out.2 http://www.ks.uiuc.edu/Research/namd/51