[gmx-users] Restart files

David van der Spoel spoel at xray.bmc.uu.se
Sat Aug 27 19:17:21 CEST 2005

On Sat, 2005-08-27 at 13:03 -0400, Bob Johnson wrote:
> Hello everyone,
> My system involves an infinite nanotube, a single stranded DNA molecule, and
> some water. After performing several simulations, the DNA molecule drifts along
> the nanotube and half of the DNA ends up in the next periodic box. Now I want to
> add additional water molecules (or methanol molecules) to the system. When I add
> just one water molecule, it seems that the simulation loses memory of the fact
> that the DNA on one side of the box is bonded to the DNA on the other side.
> Normally when the DNA slides into the next periodic box, VMD will draw long
> bonds stretching across the nanotube connecting the truncated DNA molecule with
> the portion that now appears on the opposite side of the box. However, upon
> addition of one water molecule, no bonds are drawn. It seems that the
> simulation now treats the DNA as two truncated pieces instead of realizing that
> they are, in fact, bonded together. Eventually the simulation crashes. All I am
> doing is adding one extra water to the topology file like so,
> Initial topology file entry:
> [ molecules ]
> nanotube       1
> ssdna          1
> water        496
> Final topology file entry:
> [ molecules ]
> nanotube       1
> ssdna          1
> water        497
> I then add the coordinates of one water molecule to the restart.g96 file. I then
> perform a simulation using restart.g96 as my initial configuration. The
> simulation proceeds as I have described above. What is going on here?
You never say how you add the water. You should definitely not edit your
box size in the direction of the DNA/Tube.

> Thanks,
> Bob Johnson
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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