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

[Tsjerk Wassenaar]

Hey Justin,
> 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.

I think this is put too boldly. There are plenty of examples where
pairs from native ensembles have large RMSD: e.g., proteins in
alternative conformational states and intrinsically disordered
proteins. The RMSD doesn't say anything about 'correctness' or
'nativeness', only about (dis)similarity.
The RMSD distribution widens with denaturation, which might actually
be what was meant. In that case, large(r) RMSD values can be obtained
by raising the temperature, possibly as part of an extended sampling
scheme, such as REMD.

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands