Dear GMX Users, I am wish to perform a conformational transition simulation using coarse-grained models (SBM http://smog-server.org/). I wanted to apply flooding to explore the conformational transition and have open-close transition my trajectory. But what I find is that when I start from a open-state, the system moves to the closed-state and just stays there forever (20 ns) simulation. I use the following command. make_edi -f eigenvec.trr -eig eigenval.xvg -s 1pdb.pdb -o sam.edi -flood 7-16 -tau 0 -Eflnull 450.0 -hessian -alpha 2 -ori 1pdb.pdb -T 50
the eigenvec.trr was generated from anisotropic network models. How should I organize the different parameters to effect this transition. As of now I am executing my commands (and also my understanding) are based on the following paper: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20473/abstract Best, nahren -- 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
