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Running music (explained with MD of butane as example)

Please repeat this example before proceeding. If you get stuck here that means you are making some simple mistakes. Also, checkout the bugs/mistakes site before asking any questions. All the files used for this example are taken from MD of Butane section in the Examples section. So copy them to your working directory before proceeding.

If you are reasonably familiar with Molecular Simulations and Linux, you may just read the Quickstart and skip these detailed instructions.

This is explained for an MD run. All steps are similar for other simulations like GCMC or NVTMC. Example files for all possible simulations are given in the Examplessection.

By now you have successfully compiled the code and created the executable (music.exe) using the driver music_md.F90. For convenience lets rename the executable as md.exe. Now let us try to run MD of Butane in gas phase at 300K using a united atom model. (Its assumed that you are molecular simulation person who has read some basic text book like Allen and Tildesely.) What are the information required so that md.exe knows what to do?

we need to specify things like:

Such information is passed to music through various input files. Formats of all different input files and output files are described later. Here we describe the files required for the particular case of MD of butane in gas phase. The beginning of all input start from the file that will be referred to as ``Control File''. While reading through the control file, Music will realize that some other files also are needed for this particular simulation and look for them in the current directory. Some special input files like large potential maps or molecule informations might be kept in some special directories specified by the Linux environmental variables.

It is convenient to copy all the required files into a separate directory. Assume you have placed them in $HOME/music. Change into that directory. Also copy (or link) the md.exe into this directory.

To run the Music executable, assuming you have created the control file butane_md.ctr (or copied it from the butane MD example), run the command

md.exe butane_md.ctr

Music will read in the information from the control file and run the appropriate simulation. Thus control file is the only file required for music executable to start. As it progresses through the control file it might need additional information from other input files too. By default, information about the simulation progress is written to the screen. If you wish, you can redirect that output to a file, say music.log, using,

md.exe butane_md.ctr > & music.log &

[ Linux for Dummies : The first & above implies standard-error-output is also written to music.log. Second & implies the program is run in the back ground. ] Some command-line help is available with,

    md.exe --help

One of the options being implemented is the ability for Music to produce a sample control file with the command,

    md.exe --samplecf > &

which will write the sample to Currently, this feature is only implemented for MD simulations and it might not be up to date. But it is cool and worth checking.

next up previous contents
Next: Setting the Environment Variables Up: Basics Previous: Compiling music to get
Last edited by Shaji Chempath on: 2008-06-26