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

[Liu, Liang]

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://vt.edu/Pages/Personal/justin>
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>> >
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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-- 
Best,
Liang Liu
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