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

Albert mailmd2011 at gmail.com
Wed Apr 17 07:33:54 CEST 2013

Hello Brad:

  thanks for advices.
  I've also solved the problem after I run the 6.1 minimization step in 
NAMD. After that, I reimport the lipids system into gromacs, and it no 
longer complain those issue.


On 04/16/2013 09:59 PM, Brad Van Oosten wrote:
> 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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