[gmx-users] How to obtain structures with large RMSD?

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 10 17:06:43 CEST 2011

Liu, Liang wrote:
> Hi, all,
> I am trying to use Gromacs to obtain structural ensembles around native 
> structures (PDB structures).
> However the simulated structures are always very close to the initial 
> one, with RMSD < 0.2.
> I am wondering how to obtain large-RMSD structures? Thanks.

Large RMSD values would indicate non-native structures, which doesn't sound like 
what you're looking for.  If your goal is simply enhanced sampling, try REMD.



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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