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

[Justin A. Lemkul]

Liu, Liang wrote:
> How's position restraint? If the force constant is reduced (reduce the 
> number in posre.itp ?), the simulation will lead to more flexible structure?
> 

Position restraints are inherent inhibition to structural sampling.  Their 
intent is to prevent the protein (or whatever restrained molecule) from changing 
too much.  Of course, it can change since it's only a harmonic potential, but if 
you're looking for better sampling then I would turn off any form of position 
restraints.

-Justin

> On Mon, Oct 10, 2011 at 10:20 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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>
>         <mailto: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> <http://vt.edu> | (540)
>         231-9080 <tel:%28540%29%20231-9080>
>            <tel:%28540%29%20231-9080>
>            http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
>         <http://vt.edu/Pages/Personal/justin>
>            <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 <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

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