[gmx-users] LINCS error during mdrun

[Mark Abraham]

> Dear GROMACS users,
>
>
>
> I am trying to run md of a protein with a non-standard residue.
>
> It was fine up until I ran mdrun with pr.mdp, where I received a LINCS
> warning after 20 steps (0.042 ps).
>
>
>
> Step 21, time 0.042 (ps)  LINCS WARNING

> I looked up the mailing list and found discussion about this subject but
> there appears to be no conclusions.

That's because the problem lies with your topology or your structure. Have
a look at the structures and see what is wrong. Either you need to fix the
topology, or you haven't relaxed a bad atomic contact enough.

I wish I had a dollar for every time I've given the above advice for a
LINCS error!

Mark