[AMBER] AMD with restrained molecule.

From: Binwu Zhao <bzhao.ncsu.edu>
Date: Mon, 11 May 2015 14:09:21 -0400

Dear Amber Users,

I am investigating a system containing 2 folded peptides (same sequence) stacking on top each other. The bottom chain is regarded as a template and is normally fixed in experiment. What I am trying to get here is a free energy landscape of the unfolding process of the chain on top while keeping the bottom one fixed.
The stack is pretty stable, so using conventional MD won’t let the structure escape from the minimum. Using AMD would be a way out, however, I found few AMD simulations with restrained molecules and I am not sure whether the reweighing can be accomplished if there is a fixed molecule in the system.
Has anyone got any experience on that matter? Or could you please give me some suggestions on it?

Binwu Zhao
AMBER mailing list
Received on Mon May 11 2015 - 11:30:02 PDT
Custom Search