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

[Tsjerk Wassenaar]

Hi Liang Liu,

You will never get broader sampling by adding restraints. If you want
to have broader sampling, raise the temperature or add denaturants.
But also ask yourself the question if what you think you want is what
you should be wanting. What is the actual question you're trying to
solve?

Cheers,

Tsjerk

On Mon, Oct 10, 2011 at 5:32 PM, Liu, Liang <liu4gre at gmail.com> 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?
>
> On Mon, Oct 10, 2011 at 10:20 AM, Justin A. Lemkul <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>> 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
>>
>> ========================================
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>
>
>
> --
> Best,
> Liang Liu
>
> --
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-- 
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