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

[Justin A. Lemkul]

Liu, Liang wrote:
> Thanks.
> 
> Will the constrain help?
> 

Bond constraints?  Well, in general, they're useful, and likely necessary at 
high temperature to keep your system stable.  Please be more specific.

-Justin

> On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
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> 
> 
> -- 
> Best,
> Liang Liu

-- 
========================================

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

========================================