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

[bipin singh]

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*