[gmx-users] EM problem

[Mark Abraham]

Usually this means your "doubling" didn't allow for the required space
between atoms at the boundaries. It is usually less painful for a
solute+solvent system to go back to your solute-only coordinate file,
put a box around it with editconf, replicate that with genconf, and
only then get solvent involved with genbox.

Mark

On Tue, Jun 25, 2013 at 5:25 PM, Kieu Thu Nguyen <kieuthu2212 at gmail.com> wrote:
> Dear users,
>
> How can i fix the system structure while minimizing energy ? I made a
> larger system by double a small system. But i can not continue simulation
> because the system crashed after EM. Although the small system was
> equilibrated well before doubling.
>
> Thankful for any help  and regards,
>
> Thu
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