Re: Simulating molecules in bulk water & VMD installation problems

From: Chris Harrison (
Date: Wed Aug 05 2009 - 08:53:01 CDT

You'll need to post the vmd question to the vmd-l list. Please don't
cross-post to both the vmd and namd lists the same question.

WRT your NAMD question .... forgive me perhaps failing to understand your
request, but would your problem not be solved by solvating your hexane in a
box of water, like TIP3P or similar, and then simulating?


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733               Fax: 217-244-6078
On Tue, Aug 4, 2009 at 2:27 PM, Vincent Su <> wrote:
> Hi,
> 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 = $ENV{/home/user/vmd-1.8.7/vmd}
>      25 }
>      26 if ($ENV{VMDINSTALLBINDIR}) {
>      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
> "/vmd-1.8.7/vmd"
>         (Missing operator before vmd?)
> Does anyone know what the solution is to properly install VMD?

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