[gmx-users] (no subject)

[nahren manuel]

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