Arrgh.
Correct procedure is
1) Get source code
2) Install prerequisites
3) Decide on a location from which to install, I'll call this
/source/dir - this should be in user space
3) Decide on a location into which to install, I'll call this /dest/dir
- this can be anywhere, but you need root access for some places,
including the default
4) cd to /source/dir
5) unpack gromacs sources
6) cd gromacs-3.3.1
7) configure --prefix=/install/dir
8) make
9) if needed, change to root
10) make install
11) exit root access
12) now source /dest/dir/scripts/GMXRC, or better, put it in your .cshrc
or .bashrc as appropriate and log into a new shell
13) use gromacs
This is the general procedure for any software that uses configure.
Mark
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