[gmx-users] Re: why minimization stop so fast

[Brad Van Oosten]

Hello,I have had the same problem with CHARMM-GUI however I have found a
decent work-around procedure:  1. Go to your input .gro file and locate the
atom with infinite force (atom 23533 in this case)2. Change one of the x,y,z
positions of that atom by about  /- 0.5.3. Rerun grompp with the new .gro
file5. rerun minimization4. Repeat. this may happen with several atoms that
are overlapped, but with the little shove you give it, it may be able to
correct itself



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