[gmx-users] Purpose of the pair list

David van der Spoel spoel at xray.bmc.uu.se
Sat Aug 27 14:34:14 CEST 2005

On Fri, 2005-08-26 at 18:17 -0400, Bob Johnson wrote:
> Hello everyone,
> My system consists of an infinite nanotube, a single stranded DNA molecule and
> some water molecules. I have a separate topology file (.itp file) for each
> molecule (nanotube.itp, ssdna.itp, and water.itp). I am using the Amber force
> field for the DNA and water. I am performing MD simulations with the generate
> pairs option. No pair list is specified in the nanotube and water topology
> files. However, there is a pair list in the DNA topology file.

gen_pairs is for the parameters only. You need to retain the pair list
that you have.

> Since I am using the generate pairs option, it seems that I should be able to
> get rid of the pair list in the DNA topology file. However, when I remove the
> list, some of the DNA bonds go crazy and the simulation crashes. The system is
> completely stable if I leave the DNA pair list untouched. This doesn't make
> sense to me because the generate pairs option should override any pair lists.
> Is that correct? Does anyone know why removing the pair list in the DNA would
> cause the simulation to crash?
> I generated the nanotube topology using x2top. I generated the nanotube and
> water topology using Amber's XLeap and then converted them to GROMACS format.
> My simulation uses pbc = full to simulate an infinite nanotube.
> 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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