[gmx-users] Energy Minimisation and Equilibration Problems

[Dallas B. Warren]

> Maximum force     =  9.4016180e+02 on atom 31

As has already been suggested, have you looked at the atoms listed as having the maximum force to see why?

>Addtionally, the structure of the solute is incorrect (all atoms are bonded to each other).

How are you visualising it?  If using VMD, then it guesses the bonding based on how far things are apart.  If your atoms are too close, then will appear like all bonded to each other.

Sounds to me like there is something wrong with the box / molecule.

Start with a box with only one molecule in it, see if you can equilibrate etc.  Then build up from there so you can pin down where the issue is.