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 <bipinel...@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* > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists