Getting Started - Computing a Trajectory

To compute a molecular dynamics trajectory with EGO, you need to:

1.

If you will use only the sequential version of EGO you need just a C compiler. For the parallel version make sure that either PVM, MPI or PARIX is installed on the parallel computer you are going to use. For details on PVM, MPI or PARIX we refer to corresponding documentations. Here we give only a short description how the environment for EGO should look like.

2.

install EGO on your computer. Compilation is done via a makefile written for GNU-make. So you need to install GNU-make. The executable must be called gmake and the location must be included to your PATH environment variable.

3.

provide a molecular description of your system and dynamics parameter data sets:
If you use X-PLOR the description consists of a PDB-file and a corresponding PSF-file. Dynamics parameters are given in parameter-files (e.g., param19.pro).

4.

create lis-files from your data:
EGO uses only these lis-files for molecular dynamics calculations. They are ASCII-files and contain all necessary data (molecule description, dynamics parameters, simulation parameter). Included with the EGO distribution is the utility-program xpl2lis which converts X-PLOR data to lis-data. A test data set of the protein BPTI is included in the distribution of the EGO program. We are going to use this data set as an example in our ``Getting started'' session.

5.

adapt the simulation parameters in the ASCII-file ctl.lis to your needs (time step, output directory, etc.).

6.

run it!

7.

analyze data!

Command sequences in this manual are given in Unix notation. Users of MS-DOS or other systems should substitute equivalent commands where appropriate.