[gmx-users] Minimization question

Alan Dodd anoddlad at yahoo.com
Fri Dec 23 13:36:11 CET 2005

Bonds in GROMACS don't break or form, that requires QM
calculations I think.  If the bond is broken at the
end, that probably means it was never there to begin
with - check your topology file.  Alternatively, it
could just be set too long so it looks broken, again,
check your topology file.

--- tprakci at ttnet.net.tr wrote:

> Hi gmx-users,
> I am performing minimizaiton on a co-factor. (FAD) I
> set up the topology and run the process. No problem
> for these. But at the end, the resultant structure
> shows that 2 bonds are broken. These occurs
> repeatedly and does not resolve with changing mdp
> options. I also used LINCS to keep the bonds. 
> In addition the rest of the molecule shows no
> considerable improvement.I will be glad to hear any
> contributions. Thanks.
> Mustafa Toprakci
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