[gmx-users] Energy minimalization

[Michael]

Hi Karel,

>
>  Hi all,
>
> I have a problem with energy minimalization of my system.
>
> It just don't converge (by cg or by steep) and when I visualized my 7
> helix
> protein after this step it had just 3 helixes and rest of atoms were
> diffuzed
> around them.
>
> What is wrong?
The order of the topology file and the coordinate file should be the
same.
For example if in the coordinate file helix 4 is before helix 5 so in
the topology file in the list of the molecules helix 4 should be before
helix 5.
> or What I should look for to reolve this situation?
>
> I'm undergraduate student.
>
> Thank you in advance
> Regards
> Karel Berka
>
> --
> Karel Berka
> ------------------------------
> student of Physical Chemistry
> Faculty of Natural Sciences
> Charles University, Prague
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Good Luck,
Michael.