[gmx-users] GMX to remove clashes?

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 14 22:49:22 CET 2011

Liu, Liang wrote:
> 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?

Gromacs is perfectly capable of energy minimization.  Whether or not 
minimization succeeds and gives a reasonable output is mostly dependent upon the 
feasibility of the starting structure.  If the minimization crashes, it's not 
Gromacs' fault ;)



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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