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

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 10 17:30:14 CEST 2011

Tsjerk Wassenaar wrote:
> 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.

Quite right.  I guess I just took the OP's stated desire for sampling around the 
"native structure," which considered the PDB structure itself to be "native." 
Thanks for the clarification; indeed an important point.


> 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


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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