[gmx-users] Energy Minimisation problem

[Mark Abraham]

supti mukherjee wrote:
> Dear all,
> I was minimising a protein structure. I added polar hydrogens to the 
> protein by some program and then proceeded for the energy minimisation. 
> I chose Conjugate Gradient of 1000 steps with emtol as 100. The mdrun 
> came out with the following error.
> 
> " During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
> 
> Variable ci has value -2147483648. It should have been within [ 0 .. 
> 17052 ]"
> 
> Can anybody please help me in identifying my mistake?

Try the general procedure outlined here... 
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation

Mark