The MDComm files mentioned in this section should be available in both the VMD and NAMD distributions. In the VMD distribution, they are in lib/mdcomm; in the NAMD distribution, they are in the mdcomm directory.
The important thing that must be done to configure another computer to run NAMD and to allow it to connect to VMD is to start rappd on this computer, and set up a configuration file for rappd which describes where all the various programs and daemons are located. This discussion assumes NAMD has already been installed in some location, i.e. /usr/local/bin/namd or really anywhere.
You should create a globally-executable directory to install the MDComm\ daemons and rappd data files; for example, /usr/local/lib/mdcomm. Then, copy the programs rappd and namdd from the NAMD distribution directory mdcomm/bin_ARCH (ARCH=HPUX9 if using HP-UX workstations, IRIX5 for SGI, etc) to /usr/local/lib/mdcomm/bin (or wherever the MDComm files are being installed). Finally, copy the entire directory mdcomm/rappd to /usr/local/lib/mdcomm, so that there is the a directory /usr/local/lib/mdcomm/rappd. This directory contains files with .conf extensions which are used to configure rappd. There should be at least one file there, namd.conf.
Once /usr/local/lib/mdcomm is created and the files are copied over, the last step is to edit the files in /usr/local/lib/mdcomm/rappd for your personal setup. There is a directory for each ARCH available; go to the one for the ARCH on which rappd and NAMD will run, and edit the file namd.conf. This file tells rappd where to find the NAMD executable, the namdd daemon, and what all the parameters are for NAMD. You will need to edit the following lines:
Finally, once the configuration file is set up, rappd must be started. You specify to rappd a directory which will be searched for files ending in a .conf extension, by using a command-line argument of the form -d <directory>. Each file of this form in the specified directory should contain the configuration data for a different application that rappd can possible start. In this way, there can be several different MD programs installed on a remote computer, and VMD can provide menu options for the user to choose which program to start. (Note, that version 1.1 of rappd reads all files in the specified directory, and not only those which end in .conf.) A useful script to use to start up rappd is the following (assuming ARCH=HPUX9, and rappd files are in /usr/local/lib/mdcomm; if not, change this to the proper path and ARCH):
#!/bin/sh # # brief script to start up rappd, killing the old rappd if necessary # start up new rappd if [ -x /usr/local/lib/mdcomm/bin/rappd -a -d /usr/local/lib/mdcomm/rappd ] then cd /usr/local/lib/mdcomm/bin ./rappd -d ../rappd & else echo "Cannot start new rappd." fi # end of script
Once rappd is running, you should be able to use VMD to connect to it and get a list with namd as an available MD program.