[gmx-users] on restricted MD

[Mark Abraham]

> Dear all, I am now using gromacs to run a md of protein-ligand complex. I
> have already minimized the protein-ligand energy, and I try do run the
> protein restricted MD which allows the movement of ligand and water with
> tine 20 ps. However during the restriction MD, there is warnings showing
> that the bonds  rotate more than 30 degree. Why this can happen? Does this
> violate thge meaning of restricted MD? In addition, for the coordinates,
> there is values extremely large, thus lead to the restricted process seems
> dead.
>
> Furthermore, there is some kinds of message like that:
>
> t=0.038 ps: water molecules starting at atom 4065 cannot be settled. WHy
> this can happen?
>
> In general, how to solve the above mentioned problems?

Try visualizing your trajectory. My guess is that your topology is
probably broken and that seeing it break will guide you to fix it.
Otherwise, minimize more rigorously, e.g. by minimizing after you solvate
as well.

Mark