Simulating molecules in bulk water & VMD installation problems

From: Vincent Su (
Date: Tue Aug 04 2009 - 14:27:38 CDT

Recently, I have been running simulations of hexanes in a finite space of
water. In those simulations, I had spherical boundary conditions on.
However, my next task is to run the hexanes in bulk water and am not sure
which variables i should manipulate in the .conf file to make it seem as if
it truly were in bulk water.

Also I am having trouble installing VMD on my laptop. I run linux and
followed instructions on the readme file. The area of the code that seems to
be having trouble is the following:
     24 $install_name = $ENV{/home/user/vmd-1.8.7/vmd}
     25 }
     27 $install_bin_dir = $ENV{~/vmd-1.8.7/bin}
     28 }
     30 $install_library_dir = $ENV{~/vmd-1.8.7/lib}
     31 }

When typing ./configure in the shell, I receive this error message:
Bareword found where operator expected at ./configure line 24, near
        (Missing operator before vmd?)

Does anyone know what the solution is to properly install VMD?

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