[gmx-users] GMX to remove clashes?

[Liu, Liang]

Hi, all,
I am wondering if Gromacs can do the following work?

Assuming I have a pdb file of an RNA molecule. Some atoms may be too close
or even overlap, I am wondering if Gromacs can move the atoms to reasonable
positions and remove the bad contacts? The final structure is supposed to
be the "most" stable structure with minimal energy. I know AMBER
minimization can do this work, and I am wondering if Gromacs can do the
same?

-- 
Best,
Liang Liu
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