[gmx-users] Energy Minimisation problem

[supti mukherjee]

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?
Thanks in advance.
Yours truly
Supti Mukhopadhyay
PhD Student, NIMHANS, Bangalore, India.

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