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

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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