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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