[gmx-users] Minimization question

[tprakci at ttnet.net.tr]

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