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

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

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

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

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

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 m