[gmx-users] (no subject)

P Sturzenegger s0460049 at sms.ed.ac.uk
Mon Feb 14 11:32:22 CET 2005

Dear gmx-users

Since I started to work with gromacs I have been challenged with the following
two problems:

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?

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.

I am thankful for every advice.

With best Regards

More information about the gromacs.org_gmx-users mailing list