[gmx-users] Problem in fianl step of MD

[Mark Abraham]

rituraj purohit wrote:
> Hi ..
> I am using gromacs 4.0 for simulating a protein molecule. i am getting 
> following problem during md run    [md.mdp  dt =0.002 ; ps ! nsteps = 
> 100000 ; total 200.0 ps ]
> 
> t = 47.530 ps: Water molecule starting at atom 46763 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> 
> What should i have to do ? please help me..

Upgrade to a recent release of GROMACS, and check out 
http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings

Mark