From: John Stone (
Date: Tue Sep 02 2008 - 16:16:49 CDT

  It's not clear what you did that's giving you the behavior
you are describing. Your statements are too vague to interpret.

In order for anyone to help you, we would need much more
detail about what steps you followed and what the result looks like.
It's typically a good idea to provide a link to a URL that contains
the structure files from each stage of preparation, and the final
result that exhibits the problem(s).

Don't email your structure files to the list, just post them on the
web somewhere and include a URL.

  John Stone

On Tue, Sep 02, 2008 at 11:54:47AM -0700, Rabab Toubar wrote:
> Hi,
> I am solvating a water molecule, and I always get the original water molecule outside the water box, and accordingly the water box dimensions are different than the input. Would the position of the initial molecule affect the rest of NAMD simulations? Or it is just a vmd visualization error ?
> Thanks
> Rabab

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