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Interactive Molecular Dynamics Display Using MDComm

   

VMD has the capability to work with a molecular dynamics program running on another computer, in order to display the results of a simulation as they are calculated. As new atomic coordinates are generated by the simulation process, they can be transferred directly over the network to VMD, which can then animate the molecule. A major new feature in VMD is the ability to add perturbative steering forces to a running simulation, which are incorporated directly into the dynamics calculation.

VMD uses a set of daemons and library routines to provide the communication and coordination functions necessary to allow connection to a remote application program. This set of daemons and library routines is known as MDComm,  written by Rick Kufrin of the National Center for Supercomputing Applications (NCSA)gif. A version of the MDComm library and daemons are provided in the standard VMD distribution for use on SGI workstations. The MDComm source code and documentation are also available from the MDComm anonymous ftp directory. See also the MDComm web page.

In order for VMD to work in this fashion as a graphical front end and control console for a remote molecular dynamics simulation, several things are necessary:  

For a full description of how these processes interact, we again direct you to the MDComm home page.

Once all these components are in place, you can use the graphical user interface tools in VMD to start up new MD jobs on a remote computer, view the results as they are calculated, and control the simulation parameters via VMD. You can choose to then kill the remote job, or else you can detach from simulation and leave it running. If you detach from a job, you can later reattach to that same job and resume visualizing the data at the current point in the simulation. See sections on Remote form, Sim form, remote command, and MDScope home page at MDScope WWW home page for more information.




next up previous contents index
Next: How the Connection Works Up: No Title Previous: Making Stereo Raster Images

Justin Gullingsrud
Tue Apr 6 09:22:39 CDT 1999