[gmx-users] ERROR ON POSITION RESTRAINED md

[Raj Badhan]

Hi
I've setup my protein within a water box and am running the 
position restrained md simulation using mdrun and pr.mdp.
I get the following error message:

step 0, time 0 (ps) LINCS WARNING relative constraint deviation 
after LINCS: ...followed by a list of amino acids which have rotated 
by over 30 degrees.

followed by a step 1, time 0.002....and then the simulation crashes.

I'm doing this with a dimer of a protein I am interested in.
I'm not sure what is going on, apart from the obvious, and any 
suggestions would be appreciated.
Many thanks
Raj Badhan