[gmx-users] (no subject)

David van der Spoel spoel at xray.bmc.uu.se
Mon Feb 14 16:57:42 CET 2005

On Mon, 2005-02-14 at 10:32 +0000, P Sturzenegger wrote:
> Dear gmx-users
> Since I started to work with gromacs I have been challenged with the following
> two problems:
> 1)
> I try to mimic a substrate of fcc packed atoms with grid constant a = 0.5 nm. I
> produce the x.gro file with a C-program. When I use
> genbox -cp x.gro -ci water.gro -nmol y -box x y z
> to fill in water, genbox places atoms in the octaeder spaces of my substrate,
> though the octaeder space has a diameter of only 0.07 nm.
> I tried to avoid that mistake by using the -vdwd option. But the latter seems to
> have no influence on that problem.
> What else could I try?
Are you sure it is not an Ångström versus nm. problem? If not you may
want to change the element name of your substrate into something
biological, that gromacs can relate to, or to add the file
> 2)
> I began to use gromacs on a cluster computer - and crashed it. The reason is
> that one of my simulations (that by the way produced pressure scaling warnings)
> created a log file, the size of which exceeded 400GB though I used an nstlog
> value of 0 or 100'000 and 1'000'000 calculation steps. Only the starting
> coordinates were written in the *.trr file.
Probably your simulation has  crashed without stopping. Although this is
not nice, you can probably fix it by checking the physics of your
> I am thankful for every advice.
> With best Regards
> Philip
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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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