[gmx-users] Essential dynamics (ED) sampling using make_edi

[James Starlight]

Dear collegues!

Oppositely to the Bipin Singh's question I wounder to know about the
exploring ( radius expansion) mode of EDS.  For example I define
essential
subspace from some collective coordinates and then run MD in that
subspace in exploring mode of EDS. Will the system be biased to the
some region of the collective space (like a guided-MD) or its only
some steered algorithm of reduction irrelevant degrees of freedom
(hight-frequency modes)? What parameters of EDS for time step as well
as scope should I use that my simulation be stereed-like not
biased-like ?

James

2012/12/12 Carsten Kutzner <ckutzne at gwdg.de>:
> Hi Bipin Singh,
>
> the parameters -deltaF0, -deltaF, -tau, -alpha, and -T are used only
> for flooding and have no effect in pure essential dynamics. Which coordinates
> appear in the output trajectory (*.trr, *.xtc) is exclusively controlled
> by .mdp options (i.e. the group you select there), not by the content of
> the .edi file.
>
> Best,
>   Carsten
>
>
> On Dec 11, 2012, at 6:27 PM, bipin singh <bipinelmat at gmail.com> wrote:
>
>> Hello All,
>>
>> I want to use the essential dynamics (ED) sampling  method to simulate the
>> unfolding to folding process using make_edi option of GROMACS. For this
>> task I am using -radcon option (acceptance radius contraction along the
>> first two eigenvectors towards the folded structure (b4md.gro)) of make_edi
>> as below:
>>
>> *make_edi -f eigenvec.trr -eig eigenval.xvg -s topol.tpr -tar b4md.gro
>> -radcon 1-2 -o sam.edi
>> *
>> *b4md.gro:* folded structure (C-alpha only)
>> *topol.tpr: *all atom *
>> eigenvec.trr*:from g_covar (C-alpha only)
>>
>> Is this is the correct way of doing the ED sampling...
>>
>>
>> Also I am not sure about the following:
>>
>> *1)* How to judge the correct/appropriate value for the:
>>
>>  -maxedsteps
>>
>> *2)* How to judge the appropriate values for the following parameters for
>> an Essential dynamics sampling input *(or it is neglected for ED sampling
>> and used only for flooding input ) *
>>
>> -deltaF0
>> -deltaF
>> -tau
>> -alpha
>> -T
>>
>> *3) *Will the output trajectory (produced using mdrun -ei sam.edi ) contain
>> all atoms or only the C-alpha atoms (using the above make_edi command).
>>
>> --
>> *-----------------------
>> Thanks and Regards,
>> Bipin Singh*
>> --
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>
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/grubmueller/kutzner
> http://www.mpibpc.mpg.de/grubmueller/sppexa
>
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