[gmx-users] Energy minimization

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Mar 23 13:03:13 CET 2007


This really is a bit too much. It's just as if you guys are trying to
push us over the edge. It gets so hard to stay polite at this point...

Read the archives on the gromacs user list. Search for "protein" "out
of box" or something, and you'll get plenty of hits, even some from
just a few days ago! Please do some homework before turning to a user


On 3/23/07, Александр Журавлев <beneor at mail.ru> wrote:
> Hie! When I try to make energy minimization of protein-ligand system in water box, after beginning the protein immediately moves out of water box leaving a hollow in water and ligand in the hollow, after that minimization continues. How could it be explained?
> Best regards!
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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