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 [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
