[gmx-users] Brownian dynamics]

Christian Kandt kandt at bph.ruhr-uni-bochum.de
Wed Feb 13 17:05:34 CET 2002


Hi Michel!

> I have done minimization before the dynamics.
> My starting structure is an X-ray structure with 5 ZN2+ ions placed
> randomly within a 1nm thich shell that is at least 1nm from the surface
> of the protein;

Maybe some of your ions cause the bad contacts. Have you tried checking
your input structure via RasMol? Try selecting everything that's within
e.g. 2 Å of your ZN-ions exculding the ions themselves. This might help
finding those bad overlaps.


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