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

[Carsten Kutzner]

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