From: Justin Gullingsrud (
Date: Sat Oct 09 2004 - 00:41:49 CDT


If you're going to be running your simulation in NAMD, it's safe to
edit the topology file and remove the H1-H2 bond. NAMD will ignore it
anyway, since it doesn't need the bond to do rigid waters, and your
VMD images will look better.


On Fri, 8 Oct 2004 15:35:37 -0700, mdcooper <> wrote:
> Hello,
> another question ...
> I see in the topology file that there is a H1 H2 bond required for Shake and,
> I see from:
> that NAMD will ignore it if rigid bonds is on.
> What I have done is built a solvent square and then, because of computational
> necessity, I have shrunk the solvent box to "within 12 of protien" in VMD. I
> then reran psfgen to get the psf file. When I loaded the psf file the water
> molecules turned into pretty triangles.
> Is this going to affect the MD simulation? Is there a better way of getting i
> tighter solvent layer?
> Thanks,
> matt

The spirit of Plato dies hard.  We have been unable to escape the
philosophical tradition that what we can see and measure in the world
is merely the superficial and imperfect representation of an
underlying reality.
                -- S.J. Gould, "The Mismeasure of Man"